# Illumina Connected Software ## Home - [Welcome](https://help.connected.illumina.com/readme.md): Accelerate your genomics journey with Illumina Connected Software. Unlock insights, streamline workflows, and collaborate seamlessly—all in one integrated ecosystem. - [Connected Home](https://help.connected.illumina.com/account-management/platform-home.md) - [Software Setup](https://help.connected.illumina.com/account-management/rg-registration.md) - [Software Billing](https://help.connected.illumina.com/account-management/rg-registration/software-billing.md) - [FAQ](https://help.connected.illumina.com/account-management/rg-registration/rg-faq.md): Frequently Asked Questions - [Admin Console](https://help.connected.illumina.com/account-management/admin-console.md) - [Workgroups](https://help.connected.illumina.com/account-management/admin-console/workgroups.md) - [Domain](https://help.connected.illumina.com/account-management/admin-console/domain.md) - [Usage Explorer](https://help.connected.illumina.com/account-management/usage-explorer.md) - [Custom Design Products](https://help.connected.illumina.com/custom-design/lab-management-products.md) - [Lab Management Products](https://help.connected.illumina.com/lab-management/lab-management-products.md) - [Run Set Up Products](https://help.connected.illumina.com/run-set-up/run-set-up-products.md) - [Run Workflows](https://help.connected.illumina.com/run-set-up/run-workflows.md) - [Sample Sheet](https://help.connected.illumina.com/run-set-up/overview.md) - [Sample Sheet Structure](https://help.connected.illumina.com/run-set-up/overview/sample-sheet-structure.md) - [Section Requirements](https://help.connected.illumina.com/run-set-up/overview/sample-sheet-structure/section-requirements.md) - [BCL Convert Interactive Sample Sheet](https://help.connected.illumina.com/run-set-up/overview/sample-sheet-structure/bcl-convert-interactive-sample-sheet.md) - [Intrument Settings](https://help.connected.illumina.com/run-set-up/overview/instrument-settings.md) - [NovaSeq X Settings](https://help.connected.illumina.com/run-set-up/overview/instrument-settings/novaseq-x-series-settings.md) - [NovaSeq X Sample Sheet Version History](https://help.connected.illumina.com/run-set-up/overview/instrument-settings/novaseq-x-series-settings/novaseq-x-sample-sheet-version-history.md) - [NextSeq 1000/2000 Settings](https://help.connected.illumina.com/run-set-up/overview/instrument-settings/nextseq-1000-2000-settings.md) - [NextSeq 1000/2000 Sample Sheet Version History](https://help.connected.illumina.com/run-set-up/overview/instrument-settings/nextseq-1000-2000-settings/nextseq-1000-2000-sample-sheet-version-history.md) - [Cloud Analysis Auto-launch Settings](https://help.connected.illumina.com/run-set-up/overview/auto-launch-settings.md) - [Index Orientation Guide](https://help.connected.illumina.com/run-set-up/overview/index-orientation-guide.md) - [i5 Index Orientation Table](https://help.connected.illumina.com/run-set-up/overview/index-orientation-guide/i5-index-orientation-table.md) - [Resources](https://help.connected.illumina.com/run-set-up/overview/resources.md) - [BCL Convert Parameter Usage](https://help.connected.illumina.com/run-set-up/overview/resources/bcl-convert-parameter-usage.md) - [Illumina Knowledge Help](https://help.connected.illumina.com/run-set-up/overview/resources/illumina-knowledge-help.md) - [MiSeq: Run Set Up](https://help.connected.illumina.com/run-set-up/miseq-run-setup.md) - [Analysis Products](https://help.connected.illumina.com/analysis/analysis-products.md) - [Cloud Analysis Auto-launch](https://help.connected.illumina.com/analysis/analysis_autolaunch.md) - [Sequencer Auto-launch Analyses Compatibility](https://help.connected.illumina.com/analysis/sequencer-reference.md) - [Interpretation Products](https://help.connected.illumina.com/interpretation/interpretation-products.md) - [Multiomics Products](https://help.connected.illumina.com/multiomics/multiomics-products.md) - [NovaSeq X: BCL Convert Auto-launch Analysis in Cloud](https://help.connected.illumina.com/cross-product-tutorials/novaseqx-bcl-autolaunch.md) - [NovaSeq 6000: BCL Convert Auto-launch Analysis in Cloud](https://help.connected.illumina.com/cross-product-tutorials/novaseq6000-bcl-autolaunch.md) - [NovaSeq 6000Dx: TSO 500 Auto-launch Analysis in Cloud](https://help.connected.illumina.com/cross-product-tutorials/autolaunch-novaseqdx-tso500.md) - [MiSeq: DRAGEN Amplicon and Connected Insights Auto-launch Analysis in Cloud](https://help.connected.illumina.com/cross-product-tutorials/miseq-amplicon.md) - [NextSeq 550/550Dx: TSO 500 and Connected Insights Auto-launch Analysis in Cloud](https://help.connected.illumina.com/cross-product-tutorials/nextseq550-tso500.md) - [Software Release Notes](https://help.connected.illumina.com/reference/software-release-notes.md): This page includes release notes for Account Management, which apply to all software products. For release notes related to a specific product, please refer to that product's documentation site. - [Documentation Revision History](https://help.connected.illumina.com/reference/document-revision-history.md) ## Design Studio Array - [Welcome to DesignStudio Array](https://help.connected.illumina.com/design-studio-array/overview/readme.md) - [Get Started](https://help.connected.illumina.com/design-studio-array/overview/get-started.md) - [Download Files](https://help.connected.illumina.com/design-studio-array/overview/download-files.md) - [Assay Design](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design.md) - [Design the Assay](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/design-assay.md) - [Review Design Summary](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/review-design.md) - [Add Custom Content to Commercial Arrays](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/add-custom.md) - [Input Target Files](https://help.connected.illumina.com/design-studio-array/product-guides/input-target-files.md) - [Output Files](https://help.connected.illumina.com/design-studio-array/product-guides/output-files.md) - [Target Files Error Code](https://help.connected.illumina.com/design-studio-array/product-guides/output-files/target-files-error-code.md) - [Target Files Common Errors](https://help.connected.illumina.com/design-studio-array/product-guides/output-files/target-files-common-errors.md) - [View or Delete Designs](https://help.connected.illumina.com/design-studio-array/product-guides/view-delete-designs.md) - [Arrays finder](https://help.connected.illumina.com/design-studio-array/product-guides/arrays-finder.md): Match up to 50k variants or genomic loci to Illumina commercial base content and download overlap results. - [Additional Resources](https://help.connected.illumina.com/design-studio-array/reference/additional-resources.md) - [Frequently Asked Questions](https://help.connected.illumina.com/design-studio-array/reference/frequently-asked-questions.md) - [Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes.md) - [DesignStudio Array v2.1.0 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v2.1.0-release-notes.md) - [DesignStudio Array v2.2.0 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v2.2.0-release-notes.md) - [DesignStudio Array v2.2.1 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v2.2.0-release-notes/designstudio-array-v2.2.1-release-notes.md) - [DesignStudio Array v3.0 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v3.0-release-notes.md): Version DSA 3.0 delivers the Methylation Release, introducing major enhancements to probe design workflows, expanded Illumina Connected Analytics (ICA) integration, improved performance, and numerous. - [DesignStudio Array v3.0.1 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v3.0-release-notes/designstudio-array-v3.0.1-release-notes.md) - [DesignStudio Array v3.1.0 Release Notes](https://help.connected.illumina.com/design-studio-array/reference/release-notes/designstudio-array-v3.1.0-release-notes.md) - [Revision History](https://help.connected.illumina.com/design-studio-array/reference/revision-history.md) ## Clarity LIMS - [Announcements](https://help.connected.illumina.com/clarity-lims/announcements/announcement.md) - [Security Bulletin](https://help.connected.illumina.com/clarity-lims/announcements/announcement/security-bulletin.md) - [Investigation of OpenSSH vulnerability with Clarity LIMS](https://help.connected.illumina.com/clarity-lims/announcements/announcement/security-bulletin/investigation-of-openssh-vulnerability-with-clarity-lims.md) - [Customer Notifications](https://help.connected.illumina.com/clarity-lims/announcements/announcement/customer-notifications.md) - [17 July 2025 Clarity LIMS Hosted Instance Interruption - Resolved](https://help.connected.illumina.com/clarity-lims/announcements/announcement/customer-notifications/2025-july-17-clarity-lims-hosted-instance-interruption-resolved.md) - [Clarity & LabLink](https://help.connected.illumina.com/clarity-lims/clarity-lims/clarity-and-lablink.md) - [API Portal](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs.md) - [REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest.md) - [REST General Concepts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/rest-general-concepts.md) - [REST Web Services](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/rest-web-services.md) - [HTTP Response Codes and Errors](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/http-response-codes-and-errors.md) - [XML UTF-8 Character Encoding](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/xml-utf-8-character-encoding.md) - [Requesting API Version Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/requesting-api-version-information.md) - [Viewing Paginated List Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/viewing-paginated-list-resources.md) - [Filtering List Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/filtering-list-resources.md) - [Working with User-Defined Fields (UDF) and Types (UDT)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/working-with-user-defined-fields-udf-and-types-udt.md) - [Traversing a Genealogy](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/traversing-a-genealogy.md) - [Working with Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/working-with-batch-resources.md) - [Getting Started with API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api.md) - [Understanding API Terminology (LIMS v5 and later)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/understanding-api-terminology-lims-v5-and-later.md) - [API-Based URIs (LIMS v4 and later)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/api-based-uris-lims-v4-and-later.md) - [Development Prerequisites](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/development-prerequisites.md) - [Structure of REST Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/structure-of-rest-resources.md) - [The Life Cycle of a Sample: Stages Versus Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/the-life-cycle-of-a-sample-stages-versus-steps.md) - [Integrating Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/integrating-scripts.md) - [Automation](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation.md) - [Automation Triggers and Command Line Calls](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-triggers-and-command-line-calls.md) - [Automation Execution Environment](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-execution-environment.md) - [Supported Command Line Interpreters](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/supported-command-line-interpreters.md) - [Automation Channels](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-channels.md) - [Error Handling](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/error-handling.md) - [Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens.md) - [Derived Sample Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/derived-sample-automation-tokens.md) - [Step Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/step-automation-tokens.md) - [Project Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/project-automation-tokens.md) - [Automation Testing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-testing.md) - [Troubleshooting Automation](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/troubleshooting-automation.md) - [Tips and Tricks](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks.md) - [Accessing Step UDFs from a different Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/accessing-step-udfs-from-a-different-step.md) - [Obfuscating Sensitive Data in Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/obfuscating-sensitive-data-in-scripts.md) - [Integrating Clarity LIMS with Upstream Sample Accessioning Systems](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/integrating-clarity-lims-with-upstream-sample-accessioning-systems.md) - [Creating Samples and Projects via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/creating-samples-and-projects-via-the-api.md) - [Displaying Files From an Earlier Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/displaying-files-from-an-earlier-step.md) - [Transitioning Output Artifacts into the Next Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/transitioning-output-artifacts-into-the-next-step.md) - [Determining the Workflow(s) to Which a Sample is Assigned](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/determining-the-workflow-s-to-which-a-sample-is-assigned.md) - [Standardizing Sample Naming via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/standardizing-sample-naming-via-the-api.md) - [Copying UDF Values from Source to Destination](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/copying-udf-values-from-source-to-destination.md) - [Updating Preset Value of a Step UDF through API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/updating-preset-value-of-a-step-udf-through-api.md) - [Automating BCL Conversion](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/automating-bcl-conversion.md) - [Finding QC Flags in Aggregate QC (Library Validation) via REST API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/finding-qc-flags-in-aggregate-qc-library-validation-via-rest-api.md) - [Setting the Value of a QC Flag on an Artifact](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/setting-the-value-of-a-qc-flag-on-an-artifact.md) - [Creating Notifications When Files are Added via LabLink](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/creating-notifications-when-files-are-added-via-lablink.md) - [Remote HTTP Filestore Setup](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/remote-http-filestore-setup.md) - [Cookbook](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook.md) - [Get Started with the Cookbook](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook.md) - [Tips and Troubleshooting](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/tips-and-troubleshooting.md): This article provides hints and tips to help you get the most out of the Cookbook recipes included in this section. - [Obtain and Use the REST API Utility Classes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/obtain-and-use-the-rest-api-utility-classes.md) - [Work with EPP/Automation and Files](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files.md) - [Automation Trigger Configuration](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/automation-trigger-configuration.md) - [Process Execution with EPP/Automation Support](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/process-execution-with-epp-automation-support.md) - [Work with Submitted Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples.md) - [Adding Samples to the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/adding-samples-to-the-system.md) - [Renaming Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/renaming-samples.md) - [Assigning Samples to Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/assigning-samples-to-workflows.md) - [Updating Sample Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/updating-sample-information.md) - [Show the Relationship Between Samples and Analyte Artifacts (Derived Samples)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/show-the-relationship-between-samples-and-analyte-artifacts-derived-samples.md) - [Work with Containers](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers.md) - [Add an Empty Container to the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/add-an-empty-container-to-the-system.md) - [Find the Contents of a Well Location in a Container](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/find-the-contents-of-a-well-location-in-a-container.md) - [Filter Containers by Name](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/filter-containers-by-name.md) - [Work with Derived Sample Automations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations.md) - [Remove Samples from Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/remove-samples-from-workflows.md) - [Requeue Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/requeue-samples.md) - [Rearray Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/rearray-samples.md) - [Work with Process/Step Outputs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs.md) - [Update UDF/Custom Field Values for a Derived Sample Output](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/update-udf-custom-field-values-for-a-derived-sample-output.md) - [Rename Derived Samples Using the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/rename-derived-samples-using-the-api.md) - [Find the Container Location of a Derived Sample](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/find-the-container-location-of-a-derived-sample.md) - [Traverse a Pooled and Demultiplexed Sample History/Genealogy](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/traverse-a-pooled-and-demultiplexed-sample-history-genealogy.md) - [View the Inputs and Outputs of a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/view-the-inputs-and-outputs-of-a-process-step.md) - [Work with Projects and Accounts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts.md) - [Remove Information from a Project](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/remove-information-from-a-project.md) - [Add a New Project to the System with UDF/Custom Field Value](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/add-a-new-project-to-the-system-with-udf-custom-field-value.md) - [Get a Project Name](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/get-a-project-name.md) - [Find an Account Registered in the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/find-an-account-registered-in-the-system.md) - [Update Contact (User and Client) Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/update-contact-user-and-client-information.md) - [Work with Multiplexing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing.md) - [Find the Index Sequence for a Reagent Label](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/find-the-index-sequence-for-a-reagent-label.md) - [Demultiplexing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/demultiplexing.md) - [Pool Samples with Reagent Labels](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/pool-samples-with-reagent-labels.md) - [Apply Reagent Labels with REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-with-rest.md) - [Apply Reagent Labels When Samples are Imported](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-when-samples-are-imported.md) - [Apply Reagent Labels by Adding Reagents to Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-by-adding-reagents-to-samples.md) - [Working with User Defined Fields/Custom Fields](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields.md) - [About UDFs/Custom Fields and UDTs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/about-udfs-custom-fields-and-udts.md) - [Performing Post-Step Calculations with Custom Fields/UDFs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/performing-post-step-calculations-with-custom-fields-udfs.md) - [Work with Processes/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps.md) - [Filter Processes by Date and Type](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/filter-processes-by-date-and-type.md) - [Find Terminal Processes/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/find-terminal-processes-steps.md) - [Run a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/run-a-process-step.md) - [Update UDF/Custom Field Information for a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/update-udf-custom-field-information-for-a-process-step.md) - [Work with the Steps Pooling Endpoint](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/work-with-the-steps-pooling-endpoint.md) - [Work with Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources.md) - [Introduction to Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/introduction-to-batch-resources.md) - [Update UDF/Custom Field Information with Batch Operations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/update-udf-custom-field-information-with-batch-operations.md) - [Retrieve Multiple Entities with a Single API Interaction](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/page-4.md) - [Select the Optimal Batch Size](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/page-3.md) - [Work with Files](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page.md) - [Attach a File with REST and Python](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/page-9.md) - [Attach Files Located Outside the Default File Storage Repository](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/attach-files-located-outside-the-default-file-storage-repository.md) - [Attach a File to a File Placeholder with REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/attach-a-file-to-a-file-placeholder-with-rest.md) - [Work with Controls](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-controls.md) - [Automated Removal of Controls from a Workflow](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-controls/automated-removal-of-controls-from-a-workflow.md) - [Application Examples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples.md) - [Python API Library (glsapiutil.py) Location](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-16.md) - [Scripts That Help Automate Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15.md) - [Route Artifacts Based Off a Template File](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/route-artifacts-based-off-a-template-file.md) - [Invoking bcl2fastq from BCL Conversion and Demultiplexing Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/invoking-bcl2fastq-from-bcl-conversion-and-demultiplexing-step.md) - [Email Notifications](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/email-notifications.md) - [Finishing the Current Step and Starting the Next](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/finishing-the-current-step-and-starting-the-next.md) - [Adding Downstream Samples to Additional Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/adding-downstream-samples-to-additional-workflows.md) - [Advancing/Completing a Protocol Step via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/advancing-completing-a-protocol-step-via-the-api.md) - [Setting a Default Next Action](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/setting-a-default-next-action.md) - [Automatic Placement of Samples Based on Input Plate Map (Multiple Plates)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map-multiple-plates.md) - [Automatic Placement of Samples Based on Input Plate Map](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map.md) - [Publishing Files to LabLink](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/publishing-files-to-lablink.md) - [Automatic Pooling Based on a Sample UDF/Custom Field](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-pooling-based-on-a-sample-udf-custom-field.md) - [Completing a Step Programmatically](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/completing-a-step-programmatically.md) - [Automatic Sample Placement into Existing Containers](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-sample-placement-into-existing-containers.md) - [Routing Output Artifacts to Specific Workflows/Stages](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/routing-output-artifacts-to-specific-workflows-stages.md) - [Creating Multiple Containers / Types for Placement](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/creating-multiple-containers-types-for-placement.md) - [Starting a Protocol Step via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/starting-a-protocol-step-via-the-api.md) - [Setting Quality Control Flags](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/setting-quality-control-flags.md) - [Applying Indexing Patterns to Containers Automatically](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/applying-indexing-patterns-to-containers-automatically.md) - [Assignment of Sample Next Steps Based On a UDF](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/assignment-of-sample-next-steps-based-on-a-udf.md) - [Parsing Metadata into UDFs (BCL Conversion and Demultiplexing)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/parsing-metadata-into-udfs-bcl-conversion-and-demultiplexing.md) - [Scripts That Validate Step Contents](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents.md) - [Validating Process/Step Level UDFs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/page-14.md) - [Checking That Containers Are Named Appropriately](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-that-containers-are-named-appropriately.md) - [Checking for Index Clashes Based on Index Sequence](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-for-index-clashes-based-on-index-sequence.md) - [Validating Illumina TruSeq Index Adapter Combinations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/validating-illumina-truseq-index-adapter-combinations.md) - [Scripts Triggered Outside of Workflows/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13.md) - [Repurposing a Process to Upload Indexes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/repurposing-a-process-to-upload-indexes.md) - [Adding Users in Bulk](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/adding-users-in-bulk.md) - [Moving Reagent Kits & Lots to New Clarity LIMS Server](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/moving-reagent-kits-and-lots-to-new-clarity-lims-server.md) - [Programatically Importing the Sample Submission Excel File](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/programatically-importing-the-sample-submission-excel-file.md) - [Generating an MS Excel Sample Submission Spreadsheet](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/generating-an-ms-excel-sample-submission-spreadsheet.md) - [Assigning Samples to New Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/assigning-samples-to-new-workflows.md) - [Miscellaneous Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12.md) - [Illumina LIMS Integration](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/illumina-lims-integration.md) - [Generating a Hierarchical Sample History](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/generating-a-hierarchical-sample-history.md) - [Protocol-based Permissions](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/protocol-based-permissions.md) - [Self-Incremental Counters](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/self-incremental-counters.md) - [Generic CSV Parser Template (Python)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/generic-csv-parser-template-python.md) - [Renaming Samples to Add an Internal ID](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/renaming-samples-to-add-an-internal-id.md) - [Creating Custom Sample Sheets](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/creating-custom-sample-sheets.md) - [Copying Output UDFs to Submitted Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/copying-output-udfs-to-submitted-samples.md) - [Parsing Sequencing Meta-Data into Clarity LIMS](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/parsing-sequencing-meta-data-into-clarity-lims.md) - [Submit to a Compute Cluster via PBS](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/submit-to-a-compute-cluster-via-pbs.md) - [Downloading a File and PDF Image Extraction](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/downloading-a-file-and-pdf-image-extraction.md) - [Resources and References](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references.md) - [Understanding LIMS ID Prefixes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/understanding-lims-id-prefixes.md) - [Container States](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/container-states.md) - [Useful Tools](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/useful-tools.md) - [Unsupported Artifact Types](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/unsupported-artifact-types.md) - [Unsupported Process Types](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/unsupported-process-types.md) - [Suggested Reading](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/suggested-reading.md) - [API Training Videos](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/api-training-videos.md) - [IPP v2.12](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.12.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.12/ipp-v2.12.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.12/ipp-v2.12.0-installation-and-user-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.12/ipp-v2.12.0-manual-upgrade.md) - [IPP v2.11](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.11.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.11/ipp-v2.11.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.11/ipp-v2.11.0-installation-and-user-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.11/ipp-v2.11.0-manual-upgrade.md) - [IPP v2.10](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.10.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.10/ipp-v2.10.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.10/ipp-v2.10.0-installation-and-user-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.10/ipp-v2.10.0-manual-upgrade.md) - [IPP v2.9](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.9.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.9/ipp-v2.9.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.9/ipp-v2.9.0-installation-and-user-configuration.md) - [IPP v2.8](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.8.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.8/ipp-v2.8.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.8/ipp-v2.8.0-installation-and-user-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.8/ipp-v2.8.0-manual-upgrade.md) - [IPP v2.7](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.7.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.7/ipp-v2.7.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.7/ipp-v2.7.0-installation-and-user-configuration.md) - [IPP v2.6](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.6.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.6/ipp-v2.6.0-release-notes.md) - [Installation and User Configuration](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.6/ipp-v2.6.0-installation-and-user-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/illumina-preset-protocols/ipp-v2.6/ipp-v2.6.0-manual-upgrade.md) - [QC and Sample Prep](https://help.connected.illumina.com/clarity-lims/sample-prep/qc-and-sample-prep.md) - [DNA Initial QC 5.1.2](https://help.connected.illumina.com/clarity-lims/sample-prep/qc-and-sample-prep/qc-dna-v5.1.2.md) - [RNA Initial QC 5.1.2](https://help.connected.illumina.com/clarity-lims/sample-prep/qc-and-sample-prep/qc-rna-v5.1.2.md) - [Library Validation QC 5.1.2](https://help.connected.illumina.com/clarity-lims/sample-prep/qc-and-sample-prep/qc-lib-v5.1.2.md) - [AmpliSeq for Illumina](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq.md) - [BRCA Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/brca-panel.md) - [Library Preparation v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/brca-panel/ampliseq-brca-lib-prep-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/brca-panel/ampliseq-brca-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/brca-panel/ampliseq-brca-std-v1.1.md) - [Cancer HotSpot Panel v2](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/cancer-hotspot-panel-v2.md) - [Library Preparation v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/cancer-hotspot-panel-v2/ampliseq-hotspot-v2-lib-prep-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/cancer-hotspot-panel-v2/ampliseq-hotspot-v2-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/cancer-hotspot-panel-v2/ampliseq-hotspot-v2-std-v1.1.md) - [Childhood Cancer Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/childhood-cancer-panel.md) - [DNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/childhood-cancer-panel/ampliseq-childhood-dna-v1.1.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/childhood-cancer-panel/ampliseq-childhood-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/childhood-cancer-panel/ampliseq-childhood-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/childhood-cancer-panel/ampliseq-childhood-std-v1.1.md) - [Comprehensive Cancer Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-cancer-panel.md) - [Library Preparation v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-cancer-panel/ampliseq-ccp-lib-prep-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-cancer-panel/ampliseq-ccp-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-cancer-panel/ampliseq-ccp-std-v1.1.md) - [Comprehensive Panel v3](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-panel-v3.md) - [DNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-panel-v3/ampliseq-cp-v3-dna-v1.1.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-panel-v3/ampliseq-cp-v3-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-panel-v3/ampliseq-cp-v3-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/comprehensive-panel-v3/ampliseq-cp-v3-std-v1.1.md) - [Custom DNA Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/custom-dna-panel.md) - [Library Preparation v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/custom-dna-panel/ampliseq-custom-lib-prep-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/custom-dna-panel/ampliseq-custom-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/custom-dna-panel/ampliseq-custom-std-v1.1.md) - [Focus Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel.md) - [DNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/ampliseq-focus-dna-v1.1.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/ampliseq-focus-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/ampliseq-focus-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/ampliseq-focus-std-v1.1.md) - [Immune Repertoire Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-repertoire-panel.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-repertoire-panel/ampliseq-repertoire-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-repertoire-panel/ampliseq-repertoire-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-repertoire-panel/ampliseq-repertoire-std-v1.1.md) - [Immune Response Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-response-panel.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-response-panel/ampliseq-response-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-response-panel/ampliseq-response-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/immune-response-panel/ampliseq-response-std-v1.1.md) - [Myeloid Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/myeloid-panel.md) - [DNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/myeloid-panel/ampliseq-mye-dna-v1.1.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/myeloid-panel/ampliseq-mye-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/myeloid-panel/ampliseq-mye-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/myeloid-panel/ampliseq-mye-std-v1.1.md) - [TCR beta-SR Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/tcr-beta-sr-panel.md) - [DNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/tcr-beta-sr-panel/ampliseq-tcr-dna-v1.1.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/tcr-beta-sr-panel/ampliseq-tcr-rna-v1.1.md) - [Transcriptome Human Gene Expression Panel](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/transcriptome-human-gene-expression-panel.md) - [RNA Library Prep v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/transcriptome-human-gene-expression-panel/ampliseq-transc-rna-v1.1.md) - [Equalizer v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/transcriptome-human-gene-expression-panel/ampliseq-transc-equ-v1.1.md) - [Standard v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/transcriptome-human-gene-expression-panel/ampliseq-transc-std-v1.1.md) - [Library Prep Validation](https://help.connected.illumina.com/clarity-lims/library-prep/run-library-prep-validation.md) - [Nextera](https://help.connected.illumina.com/clarity-lims/library-prep/nextera.md) - [Nextera Mate Pair v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/nextera/nextera-mate-pair-v1.0.md) - [Nextera Rapid Capture Custom Enrichment v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/nextera/nextera-rapid-capture-custom-enrichment-v2.0.md) - [Nextera XT v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/nextera/nextera-xt-v2.0.md) - [Targeted Enrichment](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment.md) - [Illumina DNA Prep with Enrichment (S) Tagmentation v1.2](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/dna-prep-enrich-s-tag-v1.2.md) - [Illumina RNA Prep with Enrichment (L) Tagmentation v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/rna-prep-enrich-l-tag-v1.1.md) - [TruSeq](https://help.connected.illumina.com/clarity-lims/library-prep/truseq.md) - [TruSeq ChIP-Seq v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-chip-seq-v1.0.md) - [TruSeq Custom Amplicon v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-custom-amplicon-v1.0.md) - [TruSeq DNA Exome v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-dna-exome-v2.0.md) - [TruSeq DNA PCR-Free v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-dna-pcr-free-v2.0.md) - [TruSeq Methyl Capture EPIC v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-methyl-capture-epic-v2.0.md) - [TruSeq Nano DNA v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-nano-dna-v1.0.md) - [TruSeq RNA Access v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-rna-access-v2.0.md) - [TruSeq RNA Exome v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-rna-exome-v1.0.md) - [TruSeq Small RNA v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-small-rna-v1.0.md) - [TruSeq Stranded mRNA v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-stranded-mrna-v2.1.md) - [TruSight](https://help.connected.illumina.com/clarity-lims/library-prep/trusight.md) - [TruSight Oncology 500 ctDNA v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/trusight-oncology-500-ctdna-v1.1.md) - [TruSight Oncology 500 HT v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/trusight-oncology-500-ht-v1.1.md) - [TruSight Oncology 500 v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/trusight-oncology-500-v1.1.md) - [TruSight Tumor 170 v2.0](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/trusight-tumor-170-v2.0.md) - [Other DNA Protocols](https://help.connected.illumina.com/clarity-lims/library-prep/other-dna-protocols.md) - [Illumina DNA PCR-Free Library Prep Manual v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/other-dna-protocols/dna-pcr-v1.1.md) - [Illumina DNA Prep (M) Tagmentation v1.0](https://help.connected.illumina.com/clarity-lims/library-prep/other-dna-protocols/dna-prep-m-tag-v1.0.md) - [Other RNA Protocols](https://help.connected.illumina.com/clarity-lims/library-prep/other-rna-protocols.md) - [Illumina Stranded mRNA Prep Ligation 1.1](https://help.connected.illumina.com/clarity-lims/library-prep/other-rna-protocols/mrna-ligation-v1.1.md) - [Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1](https://help.connected.illumina.com/clarity-lims/library-prep/other-rna-protocols/rna-ligation-ribo-v1.1.md) - [iLASS](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass.md) - [iLASS Infinium Genotyping v1.1](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.1.0.md) - [iLASS Infinium Batch DNA v1.1](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.1.0/ilass-infinium-batch-dna-v1.1.0.md) - [iLASS Infinium Genotyping Assay v1.1](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.1.0/ilass-infinium-genotyping-assay-v1.1.0.md) - [iLASS Infinium Genotyping with PGx Assay v1.1](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.1.0/ilass-infinium-genotyping-assay-pgx-v1.1.0.md) - [iLASS Infinium Genotyping v1.0](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.0.0.md) - [iLASS Infinium Genotyping Assay v1.0](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.0.0/ilass-infinium-genotyping-assay-v1.0.0.md) - [iLASS Infinium Genotyping with PGx Assay v1.0](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.0.0/ilass-infinium-genotyping-assay-pgx-v1.0.0.md) - [Infinium Arrays](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays.md) - [Infinium HD Methylation Assay Manual v1.2](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-hd-v1.2.md) - [Infinium HTS Assay Manual v1.2](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-hts-v1.2.md) - [Infinium LCG Assay Manual v1.2](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-lcg-v1.2.md) - [Infinium XT Assay Manual v1.2](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-xt-v1.2.md) - [GenomeStudio v1.0](https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-genome-studio-v1.0.md) - [IGA](https://help.connected.illumina.com/clarity-lims/applications/iga.md) - [IGA v2.1](https://help.connected.illumina.com/clarity-lims/applications/iga/iga-v2.1.md) - [IGA Library Prep Automated v2.1](https://help.connected.illumina.com/clarity-lims/applications/iga/iga-v2.1/iga-library-prep-automated-v2.1.md) - [IGA NovaSeq Sequencing v2.1](https://help.connected.illumina.com/clarity-lims/applications/iga/iga-v2.1/iga-novaseq-sequencing-v2.1.md) - [IGA v3.0](https://help.connected.illumina.com/clarity-lims/applications/iga/iga-v3.0.md) - [IGA Library Prep Automated v3.0](https://help.connected.illumina.com/clarity-lims/applications/iga/iga-v3.0/iga-library-prep-automated-v3.0.md) - [Viral Pathogen Protocols](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols.md) - [CDC COVID-19 RT-PCR](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr.md) - [Sort Specimens to Extraction v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-sort-v1.1.md) - [Qiagen QIAamp DSP Viral RNA Mini Kit v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-qiagen-qiamp-v1.1.md) - [Qiagen EZ1 Advanced XL v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-qiagen-ez1-v1.1.md) - [Roche MagNA Pure LC v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-roche-lc-v1.1.md) - [Roche MagNA Pure Compact v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-roche-compact-v1.1.md) - [Roche MagNA Pure 96 v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-roche-96-v1.1.md) - [bioMerieux NucliSENS easyMAG Instrument v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-biomerieux-nuclisens-v1.1.md) - [bioMerieux EMAG Instrument v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-biomerieux-emag-v1.1.md) - [Real-Time RT-PCR Prep v1.1](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-rt-pcr-v1.1.md) - [Illumina COVIDSeq v1.6](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/covid-illumina-covidseq-v1.6.md) - [Respiratory Virus Panel v1.0](https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/covid-respiratory-virus-panel-v1.0.md) - [Compatibility](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/compatibility.md) - [Integration Properties](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/integration-properties-update.md) - [Integration Properties Details](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/integration-properties-update/integration-properties-details.md) - [Clarity LIMS Product Analytics](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa.md) - [Supported Workflows](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/upa-supported-workflows.md) - [Workflow Customization](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/upa-workflow-customization.md) - [Clarity LIMS Product Analytics v1.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.5.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.5.0/upa-v1.5.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.5.0/upa-v1.5.0-configuration.md) - [Clarity LIMS Product Analytics v1.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.4.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.4.0/upa-v1.4.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.4.0/upa-v1.4.0-configuration.md) - [Clarity LIMS Product Analytics v1.3.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.1.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.1/upa-v1.3.1-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.1/upa-v1.3.1-configuration.md) - [Clarity LIMS Product Analytics v1.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.0/upa-v1.3.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.3.0/upa-v1.3.0-configuration.md) - [Clarity LIMS Product Analytics v1.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.2.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.2.0/upa-v1.2.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/clarity-lims-product-analytics-v1.2.0/upa-v1.2.0-configuration.md) - [Illumina Run Manager](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm.md) - [TLS Certificate Renewal FAQ](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/irm-update-tls-certificate.md) - [User Interaction](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/irm-user-interaction.md) - [Illumina Run Manager v1.1.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.1.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.1/irm-v1.1.1-release-notes.md) - [Installation and User Interaction](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.1/irm-v1.1.1-installation.md) - [Illumina Run Manager v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.0/irm-v1.1.0-release-notes.md) - [Installation and User Interaction](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.1.0/irm-v1.1.0-installation.md) - [Illumina Run Manager v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.0.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.0.0/irm-v1.0.0-release-notes.md) - [Installation and User Interaction](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/irm/illumina-run-manager-v1.0.0/irm-v1.0.0-installation.md) - [iScan](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan.md) - [iScan System](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-system.md) - [iScan v1.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.2.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.2.0/iscan-v1.2.0-release-notes.md) - [BeadChip Accessioning, Imaging, and Analysis](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.2.0/iscan-v1.2.0-beadchip-accessioning-imaging-and-analysis.md) - [iScan v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.1.0/iscan-v1.1.0-release-notes.md) - [BeadChip Accessioning, Imaging, and Analysis](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.1.0/iscan-v1.1.0-beadchip-accessioning-imaging-and-analysis.md) - [iScan System v1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.0.md) - [iSeq 100 Run Setup v1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iseq-100-v1.0.md) - [MiniSeq v1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miniseq-v1.0.md) - [MiSeq](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq.md) - [MiSeq v8.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.3.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.3.0/miseq-v8.3.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.3.0/miseq-v8.3.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.3.0/miseq-v8.3.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.3.0/miseq-v8.3.0-user-interaction-validation-and-troubleshooting.md) - [MiSeq v8.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0/miseq-v8.2.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0/miseq-v8.2.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0/miseq-v8.2.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0/miseq-v8.2.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq/miseq-v8.2.0/miseq-v8.2.0-manual-upgrade.md) - [MiSeq i100](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100.md) - [MiSeq i100 Workflow & Validation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseq-i100-workflow-and-validation.md) - [MiSeq i100 Workflow & Validation v2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseq-i100-workflow-and-validation/miseq-i100-workflow-and-validation-v2.0.md) - [MiSeq i100 Series Sequencing v2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseq-i100-workflow-and-validation/miseq-i100-workflow-and-validation-v2.0/miseqi100-sequencing-v2.0.md) - [MiSeq i100 Series Sequencing v2.0 Workflow User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseq-i100-workflow-and-validation/miseq-i100-workflow-and-validation-v2.0/miseqi100-sequencing-v2.0-workflow-user-interaction-validation-troubleshooting.md) - [MiSeq i100 (On-Prem)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem.md) - [MiSeq i100 On-Prem v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.1.0/miseqi100-onprem-v1.1.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.1.0/miseqi100-onprem-v1.1.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.1.0/miseqi100-onprem-v1.1.0-configuration.md) - [MiSeq i100 On-Prem v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.0.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.0.0/miseqi100-onprem-v1.0.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.0.0/miseqi100-onprem-v1.0.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.0.0/miseqi100-onprem-v1.0.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100-onprem/miseqi100-onprem-v1.0.0/miseqi100-onprem-v1.0.0-user-interaction-validation-and-troubleshooting.md) - [MiSeq i100 (Hosted)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100.md) - [MiSeq i100 v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.1.0/miseqi100-v1.1.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.1.0/miseqi100-v1.1.0-configuration.md) - [MiSeq i100 v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.0.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.0.0/miseqi100-v1.0.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.0.0/miseqi100-v1.0.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseq-i100/miseqi100/miseqi100-v1.0.0/miseqi100-v1.0.0-user-interaction-validation-and-troubleshooting.md) - [MiSeqDx](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx.md) - [MiSeqDx Sample Sheet Generation (v1.11.0 and later)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-sample-sheet-generation.md) - [MiSeqDx v1.11.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.11.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.11.0/miseqdx-v1.11.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.11.0/miseqdx-v1.11.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.11.0/miseqdx-v1.11.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.11.0/miseqdx-v1.11.0-user-interaction-validation-and-troubleshooting.md) - [MiSeqDx v1.10.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-user-interaction-validation-and-troubleshooting.md) - [Sample Sheet Generation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-sample-sheet-generation.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/miseqdx/miseqdx-v1.10.0/miseqdx-v1.10.0-manual-upgrade.md) - [Next Generation Sequencing Package](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/release-notes.md) - [NGS Extensions v5.25.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/release-notes/ngs-v5.25.1-release-notes.md) - [NGS Extensions v5.25.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/release-notes/ngs-v5.25.0-release-notes.md) - [NGS Extensions v5.24.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/release-notes/ngs-v5.24.0-release-notes.md) - [NGS Extensions v5.23.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/release-notes/ngs-v5.23.0-release-notes.md) - [Accession Kit Lots](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-accession-kit-lots.md) - [Auto-Placement of Reagent Indexes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-auto-placement-reagent-indexes.md) - [Compute Replicate Average](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-compute-replicate-average.md) - [Copy UDFs](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-copy-udfs.md) - [Initialize Artifact UDFs](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-initialize-artifact-udfs.md) - [Label Non-Labeled Outputs](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-label-non-labeled-outputs.md) - [Linear Regression Calculation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-linear-regression-calculation.md) - [Normalization Buffer Volumes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-normalization-buffer-volumes.md) - [Process Summary Report](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-process-summary-report.md) - [Routing Script](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-routing-script.md) - [Set UDF](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-set-udf.md) - [Validate Complete Plate](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-validate-complete-plate.md) - [Validate Sample Count](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-validate-sample-count.md) - [Validate Unique Indexes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/ngs/ngs-validate-unique-indexes.md) - [NextSeq 500/550](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550.md) - [NextSeq 500/550 v2.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-manual-upgrade.md) - [NextSeq 500/550 v2.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.4.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.4.0/nextseq550-v2.4.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.4.0/nextseq550-v2.4.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.4.0/nextseq550-v2.4.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.4.0/nextseq550-v2.4.0-user-interaction-validation-and-troubleshooting.md) - [NextSeq 500/550 v2.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.3.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.3.0/nextseq550-v2.3.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.3.0/nextseq550-v2.3.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.3.0/nextseq550-v2.3.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.3.0/nextseq550-v2.3.0-user-interaction-validation-and-troubleshooting.md) - [NextSeq 1000/2000 (Hosted)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k.md) - [NextSeq 1000/2000 v2.6.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.6.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.6.0/nextseq1k2k-v2.6.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.6.0/nextseq1k2k-v2.6.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.6.0/nextseq1k2k-v2.6.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.6.0/nextseq1k2k-v2.6.0-manual-upgrade.md) - [NextSeq 1000/2000 v2.5.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.1.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.1/nextseq1k2k-v2.5.1-release-notes.md) - [NextSeq 1000/2000 v2.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.0/nextseq1k2k-v2.5.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.0/nextseq1k2k-v2.5.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.0/nextseq1k2k-v2.5.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.5.0/nextseq1k2k-v2.5.0-manual-upgrade.md) - [NextSeq 1000/2000 v2.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.4.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.4.0/nextseq1k2k-v2.4.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.4.0/nextseq1k2k-v2.4.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k/nextseq1k2k-v2.4.0/nextseq1k2k-v2.4.0-user-interaction-validation-and-troubleshooting.md) - [NextSeq 1000/2000 (On-Prem)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem.md) - [NextSeq 1000/2000 On-Prem v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.1.0/nextseq1k2k-onprem-v1.1.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.1.0/nextseq1k2k-onprem-v1.1.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.1.0/nextseq1k2k-onprem-v1.1.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.1.0/nextseq1k2k-onprem-v1.1.0-user-interaction-validation-and-troubleshooting.md) - [NextSeq 1000/2000 On-Prem v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.0.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.0.0/nextseq1k2k-onprem-v1.0.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.0.0/nextseq1k2k-onprem-v1.0.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.0.0/nextseq1k2k-onprem-v1.0.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/nextseq1k2k-onprem/nextseq1k2k-onprem-v1.0.0/nextseq1k2k-onprem-v1.0.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq 6000 (API-based)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api.md) - [NovaSeq 6000 API-based v3.7.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.1-release-notes.md) - [NovaSeq 6000 API-based v3.7.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.0/novaseq6k-api-v3.7.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.0/novaseq6k-api-v3.7.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.0/novaseq6k-api-v3.7.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.7.0/novaseq6k-api-v3.7.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq 6000 API-based v3.6.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0/novaseq6k-api-v3.6.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0/novaseq6k-api-v3.6.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0/novaseq6k-api-v3.6.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0/novaseq6k-api-v3.6.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-api/novaseq6k-api-v3.6.0/novaseq6k-api-v3.6.0-manual-upgrade.md) - [NovaSeq 6000 (File-based)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file.md) - [NovaSeq 6000 File-based v2.6.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0/novaseq6k-file-v2.6.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0/novaseq6k-file-v2.6.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0/novaseq6k-file-v2.6.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0/novaseq6k-file-v2.6.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq 6000 File-based v2.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.5.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.5.0/novaseq6k-file-v2.5.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.5.0/novaseq6k-file-v2.5.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.5.0/novaseq6k-file-v2.5.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.5.0/novaseq6k-file-v2.5.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq 6000Dx (API-based)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx.md) - [NovaSeq 6000Dx API-based v1.3.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.1-release-notes.md) - [NovaSeq 6000Dx API-based v1.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.0/novaseq6kdx-v1.3.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.0/novaseq6kdx-v1.3.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.0/novaseq6kdx-v1.3.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.3.0/novaseq6kdx-v1.3.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq 6000Dx API-based v1.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.2.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.2.0/novaseq6kdx-v1.2.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.2.0/novaseq6kdx-v1.2.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.2.0/novaseq6kdx-v1.2.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6kdx/novaseq6kdx-v1.2.0/novaseq6kdx-v1.2.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq X Series](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series.md) - [NovaSeq X Series Workflow & Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseq-x-series-workflow-and-configuration.md) - [NovaSeq X Series Workflow & Configuration v2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseq-x-series-workflow-and-configuration/novaseq-x-series-workflow-and-configuration-v2.0.md) - [NovaSeq X Series Sequencing v2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseq-x-series-workflow-and-configuration/novaseq-x-series-workflow-and-configuration-v2.0/novaseq-x-series-sequencing-v2.0.md) - [NovaSeq X Series Sequencing v2.0 Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseq-x-series-workflow-and-configuration/novaseq-x-series-workflow-and-configuration-v2.0/novaseq-x-series-sequencing-v2.0-configuration.md) - [NovaSeq X Series (Hosted)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx.md) - [NovaSeq X Series v1.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.4.0-release-notes.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.4.0-release-notes/novaseqx-v1.4.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq X Series v1.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.3.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.3.0/novaseqx-v1.3.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.3.0/novaseqx-v1.3.0-configuration.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.3.0/novaseqx-v1.3.0-manual-upgrade.md) - [NovaSeq X Series v1.2.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.1.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.1/novaseqx-v1.2.1-release-notes.md) - [NovaSeq X Series v1.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.0/novaseqx-v1.2.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.0/novaseqx-v1.2.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.0/novaseqx-v1.2.0-user-interaction-validation-and-troubleshooting.md) - [Manual Upgrade](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.2.0/novaseqx-v1.2.0-manual-upgrade.md) - [NovaSeq X Series v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.1.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.1.0/novaseqx-v1.1.0-release-notes.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.1.0/novaseqx-v1.1.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.1.0/novaseqx-v1.1.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq X Series (On-Prem)](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem.md) - [NovaSeq X Series On-Prem v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.1.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.1.0-release-notes/novaseqx-onprem-v1.1.0-installation.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.1.0-release-notes/novaseqx-onprem-v1.1.0-user-interaction-validation-and-troubleshooting.md) - [NovaSeq X Series On-Prem v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.0.0.md) - [Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.0.0/novaseqx-onprem-v1.0.0-release-notes.md) - [Installation](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.0.0/novaseqx-onprem-v1.0.0-installation.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.0.0/novaseqx-onprem-v1.0.0-configuration.md) - [User Interaction, Validation and Troubleshooting](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq-x-series/novaseqx-onprem/novaseqx-onprem-v1.0.0/novaseqx-onprem-v1.0.0-user-interaction-validation-and-troubleshooting.md) - [Other Release Notes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes.md) - [IPP v2.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/ipp-v2.0.0-release-notes.md) - [IPP v2.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/ipp-v2.2.0-release-notes.md) - [IPP v2.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/ipp-v2.3.0-release-notes.md) - [IPP v2.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/ipp-v2.4.0-release-notes.md) - [IPP v2.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/ipp-v2.5.0-release-notes.md) - [iScan v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/iscan-v1.0.0-release-notes.md) - [MiSeq v6.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseq-v6.0.0-release-notes.md) - [MiSeq v6.0.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseq-v6.0.1-release-notes.md) - [MiSeq v8.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseq-v8.0.0-release-notes.md) - [MiSeq v8.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseq-v8.1.0-release-notes.md) - [MiSeqDx v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseqdx-v1.0.0-release-notes.md) - [MiSeqDx v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseqdx-v1.1.0-release-notes.md) - [MiSeqDx v1.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseqdx-v1.5.0-release-notes.md) - [MiSeqDx v1.9.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/miseqdx-v1.9.0-release-notes.md) - [NextSeq 1000/2000 v1.0.5](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v1.0.5-release-notes.md) - [NextSeq 1000/2000 v2.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.0.0-release-notes.md) - [NextSeq 1000/2000 v2.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.1.0-release-notes.md) - [NextSeq 1000/2000 v2.1.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.1.1-release-notes.md) - [NextSeq 1000/2000 v2.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.2.0-release-notes.md) - [NextSeq 1000/2000 v2.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.3.0-release-notes.md) - [NextSeq 1000/2000 v2.3.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq1k2k-v2.3.1-release-notes.md) - [NextSeq 500/550 v2.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq550-v2.0.0-release-notes.md) - [NextSeq 500/550 v2.0.3](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq550-v2.0.3-release-notes.md) - [NextSeq 500/550 v2.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq550-v2.1.0-release-notes.md) - [NextSeq 500/550 v2.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/nextseq550-v2.2.0-release-notes.md) - [NovaSeq 6000 API-based v3.2.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.2.1-release-notes.md) - [NovaSeq 6000 API-based v3.2.2](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.2.2-release-notes.md) - [NovaSeq 6000 API-based v3.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.3.0-release-notes.md) - [NovaSeq 6000 API-based v3.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.4.0-release-notes.md) - [NovaSeq 6000 API-based v3.5.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.5.0-release-notes.md) - [NovaSeq 6000 API-based v3.5.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-api-v3.5.1-release-notes.md) - [NovaSeq 6000 File-based v2.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.1.0-release-notes.md) - [NovaSeq 6000 File-based v2.2.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.2.0-release-notes.md) - [NovaSeq 6000 File-based v2.2.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.2.1-release-notes.md) - [NovaSeq 6000 File-based v2.2.2](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.2.2-release-notes.md) - [NovaSeq 6000 File-based v2.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.3.0-release-notes.md) - [NovaSeq 6000 File-based v2.4.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.4.0-release-notes.md) - [NovaSeq 6000 File-based v2.4.1](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6k-file-v2.4.1-release-notes.md) - [NovaSeq 6000Dx v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6kdx-v1.0.0-release-notes.md) - [NovaSeq 6000Dx v1.1.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseq6kdx-v1.1.0-release-notes.md) - [NovaSeq X Series v1.0.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/other-release-notes/novaseqx-v1.0.0-release-notes.md) - [References](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references.md) - [Configure Multiple Identical netPathPrefixSearch Values](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references/configure-multiple-identical-netpathprefixsearch-values.md) - [Configure Support for Samples Having Duplicate Names with Different Indexes](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references/configure-support-samples-duplicate-names-different-indexes.md) - [Illumina Instrument Sample Sheets](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references/illumina-instrument-sample-sheets.md) - [Terminology](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references/terminology.md) - [Transfer Files using Rsync Between Hosted Clarity Instance and Customer File Server For File-Based Integrations](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/references/rsync-file-transfer.md) - [Lab Instrument Toolkit](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk.md) - [Template File Generator](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-template-file-generator.md) - [Creating Template Files](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-template-file-generator/litk-creating-template-files.md) - [Template File Contents](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-template-file-generator/litk-template-file-contents.md) - [Template File Generator Troubleshooting](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-template-file-generator/litk-template-file-generator-troubleshooting.md) - [Add Blank Lines](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-add-blank-lines.md) - [Convert CSV to Excel](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-convert-csv-to-excel.md) - [Parse CSV](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-parse-csv.md) - [Name Matching XML Parser](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-name-matching-xml-parser.md) - [Sample Placement Helper](https://help.connected.illumina.com/clarity-lims/integration-toolkits/litk/litk-sample-placement-helper.md) - [Lab Logic Toolkit](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk.md) - [Working with Lab Logic Toolkit](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script.md) - [Data Collection Entities](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-data-collection-entities.md) - [Failing a Script](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-failing-a-script.md) - [Mapping Field Types](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-mapping-field-types.md) - [Non-UDF/Custom Field Properties](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-non-udf-custom-field-properties.md) - [Setting QC Flags](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-setting-qc-flags.md) - [Setting Next Actions](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-setting-next-actions.md) - [Specifying Custom Fields](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-specifying-custom-fields.md) - [Working with Submitted Samples](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-working-with-submitted-samples.md) - [Working with Containers](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-working-with-the-script/lltk-working-with-containers.md) - [Lab Logic Toolkit Script Examples](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-lab-logic-toolkit-script-examples.md) - [Comparing Stop/Start Dates and Times with LLTK](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-lab-logic-toolkit-script-examples/lltk-comparing-stop-start-dates-and-time-with-lltk.md) - [Lab Logic Toolkit FAQ](https://help.connected.illumina.com/clarity-lims/integration-toolkits/lltk/lltk-lab-logic-toolkit-faq.md) - [Integration](https://help.connected.illumina.com/clarity-lims/known-issues/integration.md) - [Sample Sheet Generation Issue and CLPA Issues When Samples Have Been Assigned QC Flag Prior to Entering Steps](https://help.connected.illumina.com/clarity-lims/known-issues/integration/set9561-sample-sheet-generation-fail-samples-with-qc.md) - [Third Party Software Information](https://help.connected.illumina.com/clarity-lims/resources/third-party-software-readme.md) - [Revision History](https://help.connected.illumina.com/clarity-lims/others/revision-history.md) * [Release Notes Clarity LIMS v6.3](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme.md) * [Additional Notes for Clarity LIMS v6.3](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/additional-notes-v6.3.x.md) * [Known Issues for Clarity LIMS v6.3](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/known-issues-v6.3.x.md) * [Release Notes Clarity LIMS v6.3.4](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/release-notes-clarity-lims-v6.3.4.md) * [Release Notes Clarity LIMS v6.3.3](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/release-notes-clarity-lims-v6.3.3.md) * [Release Notes Clarity LIMS v6.3.2](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/release-notes-clarity-lims-v6.3.2.md) * [Release Notes Clarity LIMS v6.3.1](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/release-notes-clarity-lims-v6.3.1.md) * [Release Notes Clarity LIMS v6.3.0](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/readme/release-notes-clarity-lims-v6.3.0.md) * [Technical Overview](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/technical-overview.md) * [Technical Requirements](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/technical-overview/technical-requirements.md) * [Installation](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation.md) * [Installation Procedure](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation/installation-procedure.md): This section provides instructions for installing on-premise deployments of Clarity LIMS v6.3. For assistance with installation steps, contact the Illumina Support team. * [Guide to Secret Management](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation/guide-to-secret-management.md) * [Install/Upgrade Secret Management for Integration Modules](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation/install-upgrade-secret-management-for-integration-modules.md): This section describes the installation steps required for installing Secret Utility and integration packages. * [Change the Clarity LIMS Hostname](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation/change-the-clarity-lims-hostname.md) * [Update Server Passwords and Database Connection Details](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/installation/update-server-passwords-and-database-connection-details.md): This document describes the steps required to update the Clarity LIMS application configuration. * [On-Premise Deployments](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments.md) * [Pre-installation Requirements](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/pre-installation-requirements.md) * [Install a Purchased SSL/TLS Certificate](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/pre-installation-requirements/install-a-purchased-ssl-tls-certificate.md): This section explains how to install purchased SSL/TLS certificates into Clarity LIMS v5 and later. * [Configure Your HashiCorp Vault](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/pre-installation-requirements/configure-your-hashicorp-vault.md) * [On Premise to On Premise Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/on-premise-to-on-premise-upgrade-procedures.md): This section provides instructions for upgrading an existing on premise Clarity LIMS deployment. For assistance with upgrade steps, contact the Illumina Support team. * [On Premise to On Premise In-place Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/on-premise-to-on-premise-in-place-upgrade-procedures.md): This section provides instructions for upgrading an existing on premise Clarity LIMS deployment. For assistance with upgrade steps, contact the Illumina Support team. * [On Premise to Hosted Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/on-premise-to-hosted-upgrade-procedures.md): This section provides instructions for upgrading existing on premise Clarity LIMS deployments to hosted deployments. For assistance with upgrade steps, contact the Illumina Support team. * [Hosted to On Premise Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/on-premise-deployments/hosted-to-on-premise-upgrade-procedures.md): This section provides instructions for upgrading existing hosted Clarity LIMS deployments to on premise deployments. For assistance with upgrade steps, contact the Illumina Support team. * [Administration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration.md) * [Database Cleanup Procedure](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/database-cleanup-procedure.md): This section describes the steps for removing projects, samples, workflows, protocols, steps, and other artifacts that were created during training but are not needed for production, from the system. * [Backup and Restore Procedure](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/backup-and-restore-procedure.md) * [Receiving and Decrypting Cloud Backup Data](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/receiving-and-decrypting-cloud-backup-data.md) * [LDAP Integration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/ldap-integration.md) * [Using the LDAP Checker Tool](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/ldap-integration/using-the-ldap-checker-tool.md) * [Illumina Connected Software Platform Integration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/platform-authentication-service-integration.md) * [Clarity LIMS Log Files](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/clarity-lims-log-files.md) * [Customize the Term Used for Projects](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/customize-the-term-used-for-projects.md) * [Enforcing Unique Sample Names Within a Project](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/enforcing-unique-sample-names-within-a-project.md) * [Container Name Uniqueness](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/container-name-uniqueness.md) * [Configure Electronic Signatures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/configure-electronic-signatures.md) * [Creating Enrypted Passwords](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/creating-enrypted-passwords.md) * [Config Slicer Tool](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/config-slicer-tool.md) * [Managing Configurations with Config Slicer](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/config-slicer-tool/managing-configurations-with-config-slicer.md) * [Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/config-slicer-tool/page-2.md) * [Config Slicer Use Cases](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/config-slicer-tool/page.md) * [Troubleshooting Config Slicer](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/config-slicer-tool/page-1.md) * [Audit Trail](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/audit-trail.md) * [Enabling, Validating and Disabling Audit Trail](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/audit-trail/enabling-validating-and-disabling-audit-trail.md) * [System Settings](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/system-settings.md) * [Automation Worker Nodes](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/automation-worker-nodes.md) * [Troubleshooting Automation Worker](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/administration/automation-worker-nodes/troubleshooting-automation-worker.md) * [Clarity LIMS v6.3 Reference Guide](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide.md) * [Dashboards](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/dashboards.md): The Dashboards, Projects & Samples, and Lab View screens facilitate the day-to-day tasks of the lab manager and lab scientist. * [Overview Dashboard](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/dashboards/overview-dashboard.md) * [Projects Dashboard](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/dashboards/projects-dashboard.md) * [Projects and Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples.md) * [Projects](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples/projects.md): Projects section of the Clarity LIMS Documentation discuss how to create and work with projects. * [Samples Accessioning](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples/samples-accessioning.md) * [Sample List for Batch Import](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples/samples-accessioning/sample-list-for-batch-import.md): This section describes how to add a large number of samples to the LIMS by importing a sample list - a Microsoft® Excel® \*.xls or \*.xlsx spreadsheet file. * [Guidelines and Tips for Batch Sample Import](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples/samples-accessioning/guidelines-and-tips-for-batch-sample-import.md) * [Assign and Process Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/projects-and-samples/assign-and-process-samples.md) * [Lab View](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/lab-view.md): Lab View is the main screen in Clarity LIMS. * [Requeue and Rework Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/lab-view/requeue-and-rework-samples.md) * [Storing Sample Aliquots for Later Use](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/lab-view/storing-sample-aliquots-for-later-use.md) * [Modifying Completed Step Details](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/lab-view/modifying-completed-step-details.md) * [Alert Notifications](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/lab-view/alert-notifications.md) * [Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration.md) * [Lab Work](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work.md): Use the Lab Work configuration screen to model the workflows, protocols, and master steps used in the lab on the Lab Work configuration screen. * [Steps and Master Steps](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work/steps-and-master-steps.md): Steps & Master Steps section of the LIMS Documentation explain how to create and configure steps and master steps in the LIMS. * [Step Milestones](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work/steps-and-master-steps/step-milestones.md): This section explains the relationship between milestones, master steps, and steps; shows how to access milestone configuration settings; and provides an overview of each milestone. * [Derived Sample Naming Convention Tokens](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work/steps-and-master-steps/derived-sample-naming-convention-tokens.md) * [Protocols](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work/protocols.md): In Clarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab's workflow. This section explain how to create and configure your lab protocols. * [Workflows](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/lab-work/workflows.md): In Clarity LIMS, a workflow is a set of protocols arranged in a sequence that corresponds to the way in which work is performed in the lab. This page explain how to create and configure your workflow. * [Consumables](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables.md) * [Reagents](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/reagents.md): This section describes how to add and configure the reagent kits and lots used in your lab, and enable them for use on specific master steps. * [Reagent Kit Lot Manifest for Batch Import](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/reagents/reagent-lot-manifest-for-batch-import.md): This section describes how to batch create reagent kit lot to the LIMS by importing a Reagent Kit lot list - a Microsoft® Excel® \*.xls or \*.xlsx spreadsheet file. * [Controls](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/controls.md): This section describes how to add and configure the control samples used in your lab, and enable them for use on specific master steps. * [Instruments](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/instruments.md): This section describes how to add and configure the instruments and equipment used in your lab, and associate these items with master steps. * [Labels](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/labels.md): This section describes how to add and configure label groups (reagent categories) and labels (reagent types or molecular barcodes), and enable them for use on specific master steps. * [Containers](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/consumables/containers.md): This section describes how to add and configure the containers used in your lab, and enable them for use on specific master steps. * [Custom Fields](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/custom-fields.md): In Clarity LIMS, custom fields are used to record information about a step, sample, or other LIMS component. * [User Management](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/user-management.md): The User Management configuration screen allows for viewing and managing users, clients, and accounts. * [Manage User Access](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/user-management/manage-user-access.md) * [User Roles](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/user-management/user-roles.md) * [Configured Role-Based Permissions](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/user-management/configured-role-based-permissions.md) * [User and Profile Page](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/user-management/user-and-profile-page.md): This section describes how to update some of the details associated with your profile, including your password, email address, and profile photo. * [Automations](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/automations.md): This section describes how to add and configure the three types of automations in Clarity LIMS: step automations, project automations, and derived sample automations. * [Automation Trigger Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/automations/automation-trigger-configuration.md) * [Copy Custom Fields from Step Input to Output](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/automations/copy-custom-fields-from-step-input-to-output.md) * [Template Files Associated With Automations](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/configuration/automations/template-files-associated-with-automations.md) * [Automated Quality Control](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/automated-quality-control.md) * [Configure a QC System](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/automated-quality-control/configure-a-qc-system.md) * [Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/search.md) * [Basic Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/search/basic-search.md) * [Advanced Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/search/advanced-search.md) * [Genealogy View](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/genealogy-view.md) * [System Performance](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/system-performance.md) * [Queue Performance and Usability](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/system-performance/queue-performance-and-usability.md) * [Demultiplexing API Endpoint Performance](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/system-performance/demultiplexing-api-endpoint-performance.md) * [Terms and Definitions](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/clarity-lims-v6.3-reference-guide/terms-and-definitions.md) * [LabLink v2.5 Reference Guide](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide.md) * [Project](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/project.md) * [Email Notifications for Notes](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/project/email-notifications-for-notes.md) * [Resource Materials & Contact Us](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/resource-materials-and-contact-us.md) * [Users](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/page-3.md) * [Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/page.md) * [Publishing Files and Progress](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.3-and-lablink-v2.5/lablink-v2.5-guide/page-2.md) - [Release Notes Clarity LIMS v6.2](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/readme.md): These Release Notes describe the key changes made to software components for Clarity LIMS v6.2. - [Release Notes Clarity LIMS v6.2.1](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/readme/release-notes-clarity-lims-v6.2.1.md) - [Release Notes Clarity LIMS v6.2.0](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/readme/release-notes-clarity-lims-v6.2.0.md) - [Technical Overview](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/technical-overview.md) - [Technical Requirements](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/technical-overview/technical-requirements.md) - [Installation](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments.md) - [Installation Procedure](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments/installation-procedure.md): This section provides instructions for installing on-premise or cloud hosted deployments of Clarity LIMS v6.2. For assistance with installation steps, contact the Clarity LIMS Support team. - [Guide to Secret Management](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments/guide-to-secret-management.md) - [Install/Upgrade Secret Management for Integration Modules](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments/install-upgrade-secret-management-for-integration-modules.md): This section describes the installation steps required for installing Secret Utility and integration packages. - [Change the Clarity LIMS Hostname](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments/change-the-clarity-lims-hostname.md) - [Update Server Passwords and Database Connection Details](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/on-premise-and-cloud-hosted-deployments/update-server-passwords-and-database-connection-details.md): This document describes the steps required to update the Clarity LIMS application configuration. - [On-Premise Depolyments](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide.md) - [Pre-Installation Requirements](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/pre-installation-requirements.md) - [Install a Purchased SSL/TLS Certificate](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/pre-installation-requirements/install-a-purchased-ssl-tls-certificate.md): This section explains how to install purchased SSL/TLS certificates into Clarity LIMS v5 and later. - [Configure Your HashiCorp Vault](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/pre-installation-requirements/configure-your-hashicorp-vault.md) - [On Premise to On Premise Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/on-premise-to-on-premise-upgrade-procedures.md): This section provides instructions for upgrading an existing on premise Clarity LIMS deployment. For assistance with upgrade steps, contact the Clarity LIMS Support team. - [On Premise to Cloud Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/on-premise-to-cloud-upgrade-procedures.md): This section provides instructions for upgrading existing on premise Clarity LIMS deployments to cloud hosted deployments. For assistance with upgrade steps, contact the Clarity LIMS Support team. - [Hosted to On Premise Upgrade Procedures](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/installation-and-upgrade-guide/cloud-to-on-premise-upgrade-procedures.md): This section provides instructions for upgrading existing cloud hosted Clarity LIMS deployments to on premise deployments. For assistance with upgrade steps, contact the Clarity LIMS Support team. - [Adminstration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration.md) - [Database Cleanup Procedure](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/database-cleanup-procedure.md): This section describes the steps for removing projects, samples, workflows, protocols, steps, and other artifacts that were created during training but are not needed for production, from the system. - [Receiving and Decrypting Cloud Backup Data](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/receiving-and-decrypting-cloud-backup-data.md) - [LDAP Integration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/ldap-integration.md) - [Using the LDAP Checker Tool](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/ldap-integration/using-the-ldap-checker-tool.md) - [Clarity LIMS Log Files](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/clarity-lims-log-files.md) - [Customize the Term Used for Projects](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/customize-the-term-used-for-projects.md) - [Enforcing Unique Sample Names Within a Project](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/enforcing-unique-sample-names-within-a-project.md) - [Container Name Uniqueness](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/container-name-uniqueness.md) - [Creating Enrypted Passwords](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/creating-enrypted-passwords.md) - [Config Slicer Tool](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/page-1.md) - [Managing Configurations with Config Slicer](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/page-1/managing-configurations-with-config-slicer.md) - [Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/page-1/upgrading-a-configuration-package-manifest-file-for-compatibility-with-config-slicer-v3.0.x.md) - [Config Slicer Use Cases](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/page-1/config-slicer-use-cases.md) - [Troubleshooting Config Slicer](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/page-1/troubleshooting-config-slicer.md) - [Audit Trail](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/audit-trail.md) - [Automation Worker Nodes](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/automation-worker-nodes.md) - [Troubleshooting Automation Worker](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/adminstration/automation-worker-nodes/troubleshooting-automation-worker.md) - [Clarity LIMS v6.2 Reference Guide](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide.md) - [Dashboards](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/dashboards.md): The Dashboards, Projects & Samples, and Lab View screens facilitate the day-to-day tasks of the lab manager and lab scientist. - [Overview Dashboard](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/dashboards/overview-dashboard.md) - [Projects Dashboard](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/dashboards/projects-dashboard.md) - [Projects and Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples.md) - [Projects](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples/projects.md): Projects section of the Clarity LIMS Documentation discuss how to create and work with projects. - [Samples Accessioning](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples/samples-accessioning.md) - [Sample List for Batch Import](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples/samples-accessioning/sample-list-for-batch-import.md): This section describes how to add a large number of samples to the LIMS by importing a sample list - a Microsoft® Excel® \*.xls or \*.xlsx spreadsheet file. - [Guidelines and Tips for Batch Sample Import](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples/samples-accessioning/guidelines-and-tips-for-batch-sample-import.md) - [Assign and Process Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/projects-and-samples/assign-and-process-samples.md) - [Lab View](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/lab-view.md): Lab View is the main screen in Clarity LIMS. - [Requeue and Rework Samples](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/lab-view/requeue-and-rework-samples.md) - [Storing Sample Aliquots for Later Use](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/lab-view/storing-sample-aliquots-for-later-use.md) - [Modifying Completed Step Details](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/lab-view/modifying-completed-step-details.md) - [Alert Notifications](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/lab-view/alert-notifications.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration.md) - [Lab Work](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work.md): Use the Lab Work configuration screen to model the workflows, protocols, and master steps used in the lab on the Lab Work configuration screen. - [Steps and Master Steps](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work/steps-and-master-steps.md): Steps & Master Steps section of the LIMS Documentation explain how to create and configure steps and master steps in the LIMS. - [Step Milestones](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work/steps-and-master-steps/step-milestones.md): This section explains the relationship between milestones, master steps, and steps; shows how to access milestone configuration settings; and provides an overview of each milestone. - [Derived Sample Naming Convention Tokens](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work/steps-and-master-steps/derived-sample-naming-convention-tokens.md) - [Protocols](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work/protocols.md): In Clarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab's workflow. This section explain how to create and configure your lab protocols. - [Workflows](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/lab-work/workflows.md): In Clarity LIMS, a workflow is a set of protocols arranged in a sequence that corresponds to the way in which work is performed in the lab. This page explain how to create and configure your workflow. - [Consumables](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables.md) - [Reagents](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables/reagents.md): This section describes how to add and configure the reagent kits and lots used in your lab, and enable them for use on specific master steps. - [Controls](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables/controls.md): This section describes how to add and configure the control samples used in your lab, and enable them for use on specific master steps. - [Instruments](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables/instruments.md): This section describes how to add and configure the instruments and equipment used in your lab, and associate these items with master steps. - [Labels](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables/labels.md): This section describes how to add and configure label groups (reagent categories) and labels (reagent types or molecular barcodes), and enable them for use on specific master steps. - [Containers](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/consumables/containers.md): This section describes how to add and configure the containers used in your lab, and enable them for use on specific master steps. - [Custom Fields](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/custom-fields.md): In Clarity LIMS, custom fields are used to record information about a step, sample, or other LIMS component. - [User Management](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/user-management.md): The User Management configuration screen allows for viewing and managing users, clients, and accounts. - [Manage User Access](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/user-management/manage-user-access.md) - [User Roles](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/user-management/user-roles.md) - [Configured Role-Based Permissions](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/user-management/configured-role-based-permissions.md) - [User and Profile Page](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/user-management/user-and-profile-page.md): This section describes how to update some of the details associated with your profile, including your password, email address, and profile photo. - [Automations](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/automations.md): This section describes how to add and configure the three types of automations in Clarity LIMS: step automations, project automations, and derived sample automations. - [Automation Trigger Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/automations/automation-trigger-configuration.md) - [Copy Custom Fields from Step Input to Output](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/automations/copy-custom-fields-from-step-input-to-output.md) - [Template Files Associated With Automations](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/configuration/automations/template-files-associated-with-automations.md) - [Automated Quality Control](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/automated-quality-control.md) - [Configure a QC System](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/automated-quality-control/configure-a-qc-system.md) - [Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/search.md) - [Basic Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/search/basic-search.md) - [Advanced Search](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/search/advanced-search.md) - [Genealogy View](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/genealogy-view.md) - [System Performance](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/system-performance.md) - [Queue Performance and Usability](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/system-performance/api-endpoint-performance.md) - [Demultiplexing API Endpoint Performance](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/system-performance/performance-and-usability.md) - [Terms and Definitions](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/clarity-lims-v6.2-guide/page-2.md) - [LabLink v2.4 Reference Guide](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide.md) - [Project](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/project.md) - [Email Notifications for Notes](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/project/email-notifications-for-notes.md) - [Resource Materials & Contact Us](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/resource-materials-and-contact-us.md) - [Users](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/users.md) - [Configuration](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/configuration.md) - [Publishing Files and Progress](https://help.connected.illumina.com/clarity-lims/clarity-lims-v6.2-and-lablink-v2.4/lablink-v2.4-guide/publishing-files-and-progress.md) ## BaseSpace - [Welcome](https://help.connected.illumina.com/basespace/readme.md) - [What's New](https://help.connected.illumina.com/basespace/overview/whats-new.md) - [FAQ](https://help.connected.illumina.com/basespace/overview/faq.md) - [Technical Assistance](https://help.connected.illumina.com/basespace/overview/technical-assistance.md) - [Release Notes](https://help.connected.illumina.com/basespace/overview/latest-release.md) - [Data Model](https://help.connected.illumina.com/basespace/overview/data-model.md) - [Account Types](https://help.connected.illumina.com/basespace/overview/account-types.md) - [Professional Services](https://help.connected.illumina.com/basespace/overview/professional-services.md) - [Data Automation Overview](https://help.connected.illumina.com/basespace/automate/data-automation-overview.md) - [Automatic Data Flow](https://help.connected.illumina.com/basespace/automate/automatic-data-flow.md) - [Automatic Data Aggregation](https://help.connected.illumina.com/basespace/automate/automatic-data-aggregation.md) - [Unlock Biosamples](https://help.connected.illumina.com/basespace/automate/automatic-data-aggregation/unlock-biosamples.md) - [Correct Aggregation](https://help.connected.illumina.com/basespace/automate/automatic-data-aggregation/correct-unintended-aggregation.md) - [Request A Lab Requeue](https://help.connected.illumina.com/basespace/automate/request-lab-requeue.md) - [Yield](https://help.connected.illumina.com/basespace/automate/yield.md) - [Yield Examples](https://help.connected.illumina.com/basespace/automate/yield-examples.md) - [Example 1](https://help.connected.illumina.com/basespace/automate/yield-examples/yield-example-1.md) - [Example 2](https://help.connected.illumina.com/basespace/automate/yield-examples/yield-example-2.md) - [Example 3](https://help.connected.illumina.com/basespace/automate/yield-examples/yield-example-3.md) - [Automate Lane QC](https://help.connected.illumina.com/basespace/automate/automate-lane-qc.md) - [Manual QC](https://help.connected.illumina.com/basespace/automate/manual-qc.md) - [Statuses](https://help.connected.illumina.com/basespace/automate/statuses.md) - [Import Demo Data](https://help.connected.illumina.com/basespace/manage-data/import-demo-data.md) - [Delete Data](https://help.connected.illumina.com/basespace/manage-data/delete-and-restore-data.md) - [Import Data Into Projects](https://help.connected.illumina.com/basespace/manage-data/import-data.md) - [FastQ Upload Requirements](https://help.connected.illumina.com/basespace/manage-data/import-data/fastq-upload-reqs.md) - [Download Data](https://help.connected.illumina.com/basespace/manage-data/download.md) - [Download Individual Files](https://help.connected.illumina.com/basespace/manage-data/download/download-files.md) - [Download Datasets](https://help.connected.illumina.com/basespace/manage-data/download/download-datasets.md) - [Download Run Files](https://help.connected.illumina.com/basespace/manage-data/download/download-run-files.md) - [Download Project Files](https://help.connected.illumina.com/basespace/manage-data/download/download-project-files.md) - [Download Analysis Files](https://help.connected.illumina.com/basespace/manage-data/download/download-analysis-files.md) - [Download Samples](https://help.connected.illumina.com/basespace/manage-data/download/download-samples.md) - [Copy Datasets](https://help.connected.illumina.com/basespace/manage-data/copy-datasets-to-proj.md) - [Transfer Ownership](https://help.connected.illumina.com/basespace/manage-data/transfer-ownership.md) - [Archival Storage](https://help.connected.illumina.com/basespace/manage-data/archival-storage.md) - [Automatic Data Deletion](https://help.connected.illumina.com/basespace/manage-data/automatic-data-deletion.md) - [Sample Sheets](https://help.connected.illumina.com/basespace/sequence/sample-sheets.md) - [Mapping Sequencing Runs to Biosamples](https://help.connected.illumina.com/basespace/sequence/sample-sheets/ss-mapping-runs-to-bs.md) - [Fix Indexes](https://help.connected.illumina.com/basespace/sequence/fix-indexes.md) - [Plan Runs](https://help.connected.illumina.com/basespace/sequence/plan-runs.md) - [Plan a NextSeq 1000/2000 Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run.md) - [Set up NextSeq 1000/2000 Secondary Analysis](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run/plan-analysis.md) - [Custom Noise Baseline File](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run/custom-noise-baseline-file.md) - [Plan a NovaSeq X Series Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run.md) - [Set up NovaSeq X Series Secondary Analysis](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run/novaseqx-plan-analysis.md) - [NovaSeq X Series Custom Reference File](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run/reference-files.md) - [Plan a MiSeq i100 Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/miseqi100-planned-run.md) - [Create a Custom Index Adapter Kit](https://help.connected.illumina.com/basespace/sequence/plan-runs/custom-index-adapter-kit.md) - [Import samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/import-samples.md) - [Requeue a Planned Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/requeue-planned-run.md) - [Analysis Configuration Template](https://help.connected.illumina.com/basespace/sequence/plan-runs/analysis-configuration-template.md) - [Prep Tab](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab.md) - [Create Biological Samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/create-biosamples-prep-tab.md) - [Import Biological Samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/import-biosamples-prep-tab.md) - [Prep Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/prep-libraries-prep-tab.md) - [Import Sample Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/import-sample-libraries.md) - [Set Up a Custom Library Prep Kit](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/create-custom-prep-kit.md) - [Pool Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/pool-libraries-prep-tab.md) - [Plan Run Using Prep Tab](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/plan-run-prep-tab.md) - [Neo Prep](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep.md) - [Configure](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/configure-neo-prep.md) - [Assign Wells](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/assign-wells-neo-prep.md) - [Review](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/review-neo-prep.md) - [Overview](https://help.connected.illumina.com/basespace/microarray/overview.md) - [Manage Data](https://help.connected.illumina.com/basespace/microarray/manage-data.md) - [Launch Analysis](https://help.connected.illumina.com/basespace/microarray/launch-analysis.md) - [Plan Analysis](https://help.connected.illumina.com/basespace/microarray/plan-analysis.md) - [Troubleshoot iScan Integration](https://help.connected.illumina.com/basespace/microarray/troubleshoot-iscan.md) - [Analyze Data](https://help.connected.illumina.com/basespace/analyze/analyze-data.md) - [Launching Apps](https://help.connected.illumina.com/basespace/analyze/launching-apps.md) - [Analysis Workflows](https://help.connected.illumina.com/basespace/analyze/analysis-workflows.md) - [Re-Launch Analysis](https://help.connected.illumina.com/basespace/analyze/relaunch-analysis.md) - [Auto Analysis QC](https://help.connected.illumina.com/basespace/analyze/automatic-analysis-qc.md) - [Basespace Apps](https://help.connected.illumina.com/basespace/analyze/basespace-apps.md) - [Sharing Data](https://help.connected.illumina.com/basespace/collaborate/sharing-data.md) - [Access Shared Data](https://help.connected.illumina.com/basespace/collaborate/access-shared-data.md) - [Share with Collaborators](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators.md) - [Share Analyses](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/share-analyses.md) - [Track Analysis Delivery Status](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/track-analysis-delivery-status.md) - [Share By Link](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/share-by-link.md) - [Share By Email](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/share-by-email.md) - [Manage Collaborator Access](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/manage-collaborator-access.md) - [Data Access After Share / Transfer](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/data-access-after-share-transfer.md) - [Workgroups](https://help.connected.illumina.com/basespace/collaborate/workgroups.md) - [Manage Workgroups](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups.md) - [Access Workgroups](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/access-workgroup.md) - [Create a Workgroup and Assign Admins](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/create-workgrp-assign-admin.md) - [Rename a Workgroup](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/rename-workgroup.md) - [Add Users to a Workgroup](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/add-users-to-workgroup.md) - [Remove Users from a Workgroup](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/remove-users-from-workgroup.md) - [Add Admins to a Workgroup](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/add-admins-to-workgroup.md) - [Remove Admins from a Workgroup](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/remove-admins-from-workgroup.md) - [Manage User Access](https://help.connected.illumina.com/basespace/collaborate/manage-workgroups/manage-user-access.md) - [Change Password](https://help.connected.illumina.com/basespace/manage-your-account/change-password.md) - [iCredits and Billing](https://help.connected.illumina.com/basespace/manage-your-account/icredits-and-billing.md) - [Generate Usage Reports](https://help.connected.illumina.com/basespace/manage-your-account/generate-usage-reports.md) - [Manage Enterprise Domains](https://help.connected.illumina.com/basespace/manage-your-account/manage-enterprise-domain.md) - [Global Regions](https://help.connected.illumina.com/basespace/manage-your-account/regions.md) - [Basespace API](https://help.connected.illumina.com/basespace/developer-tools/basespace-api.md) - [Biosample Workflow Files](https://help.connected.illumina.com/basespace/files-used-by-basespace/biosample-workflow-files.md) - [BAM Files](https://help.connected.illumina.com/basespace/files-used-by-basespace/bam-files.md) - [FastQ Files](https://help.connected.illumina.com/basespace/files-used-by-basespace/fastq-files.md) - [Quality Scores](https://help.connected.illumina.com/basespace/files-used-by-basespace/quality-scores.md) - [VCF Files](https://help.connected.illumina.com/basespace/files-used-by-basespace/vcf-files.md) - [gVCF Files](https://help.connected.illumina.com/basespace/files-used-by-basespace/gvcf-files.md) - [View Data](https://help.connected.illumina.com/basespace/data/view-data.md) - [View Runs](https://help.connected.illumina.com/basespace/data/view-data/view-runs.md) - [View Run Summary](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-summary.md) - [View Run Biosamples](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-biosamples.md) - [View Run Samples](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-samples.md) - [View Run Charts](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-charts.md) - [View Run Metrics](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-metrics.md) - [View Run Indexing QC](https://help.connected.illumina.com/basespace/data/view-data/view-runs/indexing-qc.md) - [View Run Samplesheet](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-samplesheet.md) - [View Run Files](https://help.connected.illumina.com/basespace/data/view-data/view-runs/run-files.md) - [View Projects](https://help.connected.illumina.com/basespace/data/view-data/view-projects.md) - [View Analyses](https://help.connected.illumina.com/basespace/data/view-data/view-analyses.md) - [View Biosamples](https://help.connected.illumina.com/basespace/data/view-data/view-biosamples.md) - [Create a Project](https://help.connected.illumina.com/basespace/projects/create-project.md) - [Edit Project Details](https://help.connected.illumina.com/basespace/projects/edit-project.md) - [Fix Sample Sheet](https://help.connected.illumina.com/basespace/runs/fix-sample-sheet.md) - [Automated Run Zipping](https://help.connected.illumina.com/basespace/runs/automated-run-zipping.md) - [Biosample Overview](https://help.connected.illumina.com/basespace/biosamples/biosamples.md) - [Manage Biosamples](https://help.connected.illumina.com/basespace/biosamples/manage-biosamples.md) - [Biosample Workflow](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow.md) - [Add Biosamples](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow/add-biosamples.md) - [Add Prep Requests](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow/add-prep-requests.md) - [Add Analysis Workflows to an Existing Biosample](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow/add-analysis-workflows-to-existing-biosamples.md) - [Schedule Multiple Analysis Workflows for a Biosample](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow/sched-mul-analysis-wrkflws-for-bs.md) - [Schedule Analysis Workflow - Multiple Biosamples](https://help.connected.illumina.com/basespace/biosamples/biosample-workflow/sched-analysis-workfl-from-mul-bs.md) - [Associating Biosamples with Projects](https://help.connected.illumina.com/basespace/biosamples/associating-bs-data-w-projs.md) - [Combine Samples](https://help.connected.illumina.com/basespace/samples/combine-samples.md) - [Copy Samples](https://help.connected.illumina.com/basespace/samples/copy-samples.md) - [Basespace CLI](https://help.connected.illumina.com/basespace/cmd-line-interfaces/basespace-cli.md) - [Introduction to Basemount](https://help.connected.illumina.com/basespace/cmd-line-interfaces/basespace-cli/introduction-to-basemount.md) - [Additional Resources](https://help.connected.illumina.com/basespace/additional-resources/additional-resources.md) - [Security Model](https://help.connected.illumina.com/basespace/additional-resources/additional-resources/security-model.md) - [Data Streaming](https://help.connected.illumina.com/basespace/additional-resources/additional-resources/data-streaming.md) - [AWS](https://help.connected.illumina.com/basespace/additional-resources/additional-resources/aws.md) - [Previous Releases](https://help.connected.illumina.com/basespace/releases/previous-releases.md) - [2026](https://help.connected.illumina.com/basespace/releases/previous-releases/2026.md) - [7.47.0 - BaseSpace Navigation Glow-Up](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.47.0.md) - [7.46.0 - Data Transfer Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.46.0.md) - [7.45.0 - Automated Workflow Error Messaging](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.45.0.md) - [7.44.0 - Interop Library Upgrades](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.44.0.md) - [7.43.0 - Copy And Merge All Samples](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.43.0.md) - [7.42.0 - BaseSpace CLI 1.7.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2026/7.42.0.md) - [2025](https://help.connected.illumina.com/basespace/releases/previous-releases/2025.md) - [7.41.0 - Run Planning Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.41.0.md) - [7.40.0 - BaseSpace Downloader 3.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.40.0.md) - [7.39.0 - BaseSpace Downloader 3.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.39.0.md) - [7.38.0 - App Deprecations](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.38.0.md) - [7.37.0 - Analysis Details "Orchestrated Analyses" Section](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.37.0.md) - [7.36.0 - Analysis Size Display](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.36.0.md) - [7.35.0 - Display Cost for Completed ICA Analyses](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.35.0.md) - [7.34.0 - Deletion of Custom Reference Genomes](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.34.0.md) - [7.33.0 - Shared BCL Convert Section](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.33.0.md) - [7.32.0 - File Preview in Search](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.32.0.md) - [7.31.0 - Usage Explorer](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.31.0.md) - [7.30.0 - Prep Tab Deprecation](https://help.connected.illumina.com/basespace/releases/previous-releases/2025/7.30.0.md) - [2024](https://help.connected.illumina.com/basespace/releases/previous-releases/2024.md) - [7.29.0 - Improved Analysis Error Reporting](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.29.0.md) - [7.28.0 - MiSeq i100 Support](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.28.0.md) - [7.27.0 - App Store Upgrade](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.27.0.md) - [7.26.0 - Prep Tab Obsolescence Notification](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.26.0.md) - [7.25.0 - Project Column in the Analysis Files Tab](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.25.0.md) - [7.24.0 - Requeue Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.24.0.md) - [7.23.0 - BaseSpace CLI v1.6.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.23.0.md) - [7.22.0 - Analysis Autolaunch for NovaSeq X Manual Mode Runs](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.22.0.md) - [7.21.0 - Improved Look and Feel](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.21.0.md) - [7.20.0 - Analysis List Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.20.0.md) - [7.19.0 - Transfer of NovaSeq X Projects](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.19.0.md) - [7.18.0 - Custom Kit Deletion](https://help.connected.illumina.com/basespace/releases/previous-releases/2024/7.18.0.md) - [2023](https://help.connected.illumina.com/basespace/releases/previous-releases/2023.md) - [7.17.0 - Deletion of Biosample Default Projects](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.17.0.md) - [7.16.0 - Transfer of NovaSeq X Runs](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.16.0.md) - [7.15.0 - Compatibility Filtering in Run Planning](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.15.0.md) - [7.14.0 - Native App Engine Update](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.14.0.md) - [7.13.0 - Sharing for NovaSeq X Runs and Analyses](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.13.0.md) - [7.12.0 - Combined New and Classic Modes](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.12.0.md) - [7.11.0 - NovaSeq X Analysis Requeue](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.11.0.md) - [7.10.0 - NovaSeq X Analysis Autolaunch Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.10.0.md) - [7.9.0 - Multi-Analysis Run Planning](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.9.0.md) - [7.8.0 - Performance Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2023/7.8.0.md) - [2022](https://help.connected.illumina.com/basespace/releases/previous-releases/2022.md) - [7.7.0 - NovaSeqX Support](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.7.0.md) - [7.6.0 - Custom Configuration Files in Microarray Analysis Setup](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.6.0.md) - [7.5.0 - Performance Enhancements](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.5.0.md) - [7.4.0 - Run Planning Enhancements](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.4.0.md) - [7.3.0 - Improve App Launch Performance](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.3.0.md) - [7.2.0 - FastQ Generation and other Bug Fixes](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.2.0.md) - [7.1.0 - FastQ Related Fixes and Performance Improvements](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.1.0.md) - [7.0.0 - Datasets and Apps Performance](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/7.0.0.md) - [6.19.0 - ICA Integration Enhancements](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/6.19.0.md) - [6.18.0 - ICA Integration with BCL Convert](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/6.18.0.md) - [6.17.0 - Preliminary ICA Integration](https://help.connected.illumina.com/basespace/releases/previous-releases/2022/6.17.0.md) - [2021](https://help.connected.illumina.com/basespace/releases/previous-releases/2021.md) - [6.16.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.16.0.md) - [6.15.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.15.0.md) - [6.14.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.14.0.md) - [6.13.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.13.0.md) - [6.12.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.12.0.md) - [6.11.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.11.0.md) - [6.10.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.10.0.md) - [6.9.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.9.0.md) - [6.8.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.8.0.md) - [6.7.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.7.0.md) - [6.6.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.6.0.md) - [6.5.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2021/6.5.0.md) - [2020](https://help.connected.illumina.com/basespace/releases/previous-releases/2020.md) - [6.4.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/6.4.0.md) - [6.3.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/6.3.0.md) - [6.2.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/6.2.0.md) - [6.1.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/6.1.0.md) - [6.0.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/6.0.0.md) - [5.46.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/5.46.0.md) - [5.45.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/5.45.0.md) - [5.44.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/5.44.0.md) - [5.43.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/5.43.0.md) - [5.42.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2020/5.42.0.md) - [2019](https://help.connected.illumina.com/basespace/releases/previous-releases/2019.md) - [5.41.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.41.0.md) - [5.40.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.40.0.md) - [5.39.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.39.0.md) - [5.38.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.38.0.md) - [5.37.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.37.0.md) - [5.36.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.36.0.md) - [5.35.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.35.0.md) - [5.34.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.34.0.md) - [5.33.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.33.0.md) - [5.32.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.32.0.md) - [5.31.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.31.0.md) - [5.30.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2019/5.30.0.md) - [2018](https://help.connected.illumina.com/basespace/releases/previous-releases/2018.md) - [5.29.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.29.0.md) - [5.28.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.28.0.md) - [5.27.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.27.0.md) - [5.26.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.26.0.md) - [5.25.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.25.0.md) - [5.24.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.24.0.md) - [5.23.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.23.0.md) - [5.22.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.22.0.md) - [5.21.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.21.1.md) - [5.21.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.21.0.md) - [5.20.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.20.0.md) - [5.19.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.19.0.md) - [5.18.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.18.0.md) - [5.17.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.17.0.md) - [5.16.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.16.0.md) - [5.15.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.15.0.md) - [5.14.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.14.0.md) - [5.13.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.13.0.md) - [5.12.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.12.0.md) - [5.11.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2018/5.11.0.md) - [2017](https://help.connected.illumina.com/basespace/releases/previous-releases/2017.md) - [5.10.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.10.0.md) - [5.9.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.9.0.md) - [5.8.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.8.0.md) - [5.7.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.7.0.md) - [5.6.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.6.0.md) - [5.5.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.5.0.md) - [5.4.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.4.0.md) - [5.3.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.3.0.md) - [5.2.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.2.0.md) - [5.1.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.1.0.md) - [5.0.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/5.0.0.md) - [4.27.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.27.0.md) - [4.26.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.26.0.md) - [4.25.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.25.0.md) - [4.24.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.24.0.md) - [4.23.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.23.0.md) - [4.22.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.22.0.md) - [4.21.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.21.0.md) - [4.20.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.20.0.md) - [4.19.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.19.0.md) - [4.18.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.18.0.md) - [4.17.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.17.0.md) - [4.16.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.16.0.md) - [4.15.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2017/4.15.0.md) - [2016](https://help.connected.illumina.com/basespace/releases/previous-releases/2016.md) - [4.14.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.14.0.md) - [4.13.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.13.0.md) - [4.12.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.12.0.md) - [4.11.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.11.0.md) - [4.10.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.10.0.md) - [4.9.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.9.0.md) - [4.8.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.8.0.md) - [4.7.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.7.0.md) - [4.6.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.6.0.md) - [4.5.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.5.0.md) - [4.4.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.4.0.md) - [4.3.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.3.0.md) - [4.2.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.2.0.md) - [4.1.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.1.0.md) - [4.0.4](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.0.4.md) - [4.0.3](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.0.3.md) - [4.0.2](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.0.2.md) - [4.0.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.0.1.md) - [4.0.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2016/4.0.0.md) - [2015](https://help.connected.illumina.com/basespace/releases/previous-releases/2015.md) - [3.23.2](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.23.2.md) - [3.23.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.23.1.md) - [3.23.0 Issues](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.23.0.issues.md) - [3.23.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.23.0.md) - [3.20.4](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.20.4.md) - [3.20.3](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.20.3.md) - [3.20.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.20.0.md) - [3.19.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.19.1.md) - [3.19.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.19.0.md) - [3.18.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.18.0.md) - [3.17.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.17.1.md) - [3.17.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.17.0.md) - [3.16.2](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.16.2.md) - [3.16.0](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.16.0.md) - [3.15.2](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.15.2.md) - [3.15.1](https://help.connected.illumina.com/basespace/releases/previous-releases/2015/3.15.1.md) - [Release notifications](https://help.connected.illumina.com/basespace/releases/notifications.md) ## DRAGEN - [Illumina® DRAGEN™ Secondary Analysis](https://help.connected.illumina.com/dragen/welcome/welcome-page.md) - [DRAGEN Applications](https://help.connected.illumina.com/dragen/welcome/key-applications.md) - [DRAGEN User Guides](https://help.connected.illumina.com/dragen/welcome/directory.md) - [Deployment Options](https://help.connected.illumina.com/dragen/welcome/deployment-options.md) * [Illumina® DRAGEN™ Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.5/overview/welcome-page.md) * [DRAGEN Applications](https://help.connected.illumina.com/dragen/dragen-v4.5/overview/key-applications.md) * [Deployment Options](https://help.connected.illumina.com/dragen/dragen-v4.5/overview/deployment-options.md) * [DRAGEN v4.5](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5.md) * [Getting Started](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/getting-started.md) * [DRAGEN Host Software](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-host-software.md) * [DRAGEN Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-host-software/dragen-platform.md) * [DRAGEN Apps](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps.md) * [DRAGEN Germline Enrichment ICA App](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-germline-enrichment-ica-app.md) * [DRAGEN Enrichment BSSH App](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-enrichment-bssh-app.md) * [DRAGEN Germline Enrichment from BCLs BSSH App](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-germline-enrichment-from-bcls-bssh-app.md) * [DRAGEN Recipes](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes.md) * [DNA Germline Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-amplicon.md) * [DNA Germline Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-panel.md) * [DNA Germline Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-panel-umi.md) * [DNA Germline WES](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wes.md) * [DNA Germline WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wes-umi.md) * [DNA Germline WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wgs.md) * [DNA Somatic Tumor-Normal Heme WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-heme-wgs.md) * [DNA Somatic Tumor-Normal MRD](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-mrd.md) * [DNA Somatic Tumor-Normal Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) * [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) * [DNA Somatic Tumor-Normal Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) * [DNA Somatic Tumor-Normal Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) * [DNA Somatic Tumor-Normal Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) * [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) * [DNA Somatic Tumor-Only Heme WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) * [DNA Somatic Tumor-Only Solid Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-amplicon.md) * [DNA Somatic Tumor-Only Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) * [DNA Somatic Tumor-Only Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) * [DNA Somatic Tumor-Only Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) * [DNA Somatic Tumor-Only Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) * [DNA Somatic Tumor-Only Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) * [DNA Somatic Tumor-Only Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) * [DNA Somatic Tumor-Only ctDNA Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-ctdna-amplicon.md) * [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) * [Illumina TruPath Genome WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-trupath-genome-wgs.md) * [Illumina scRNA](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-scrna.md) * [Illumina scRNA Perturb seq](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-scrna-perturb-seq.md) * [Other scRNA prep](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/other-scrna-prep.md) * [RNA Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-amplicon.md) * [RNA Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-panel.md) * [RNA WTS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-wts.md) * [5 Base DNA Germline Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-panel.md) * [5 Base DNA Germline Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-panel-umi.md) * [5 Base DNA Germline WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-wgs.md) * [5 Base DNA Somatic Tumor-Normal Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-panel.md) * [5 Base DNA Somatic Tumor-Normal Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-wgs.md) * [5 Base DNA Somatic Tumor-Only Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel.md) * [5 Base DNA Somatic Tumor-Only Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel-umi.md) * [5 Base DNA Somatic Tumor-Only Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs.md) * [5 Base DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md) * [DRAGEN WGS Germline Accuracy](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline.md) * [Small Variants](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/small_variants_accuracy.md) * [Copy Number Variation](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/copy_number_variation_accuracy.md) * [Structural Variants](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/structural_variants_accuracy.md) * [HLA Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/hla_genotyping_accuracy.md) * [Targeted Callers](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/targeted_callers_accuracy.md) * [Multi-Region Joint Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/mrjd_accuracy.md) * [Ploidy Estimator](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/ploidy_estimator_accuracy.md) * [Tandem Repeats](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/tandem_repeats_accuracy.md) * [DRAGEN Reference Support](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-reference-support.md) * [Prepare a Reference Genome](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-reference-support/prepare-a-reference-genome.md) * [DRAGEN DNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline.md) * [DNA Mapping](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/dna-map-align.md) * [Read Trimming](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/read-trimming.md) * [Sorting and Duplicate Marking](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sort-dupmark.md) * [Small Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling.md) * [ROH Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/roh-caller.md) * [B-Allele Frequency Output](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/baf-output.md) * [Somatic Mode](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) * [Somatic ML for Small VC (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/somatic-mode/somatic-ml.md) * [Pedigree Analysis](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/pedigree-analysis.md) * [De Novo Small Variant Filtering](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/filtering.md) * [Autogenerated MD5SUM for VCF Files](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) * [Force Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) * [Machine Learning for Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) * [Evidence BAM](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) * [Mosaic Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) * [VCF Imputation](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) * [Multi-Region Joint Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) * [Small Variant Calling Metrics](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/small-variant-calling-metrics.md) * [Copy Number Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview.md) * [Germline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline.md) * [Germline Depth-Only](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline/cnv-germline-legacy.md) * [Somatic](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-somatic.md) * [Reference](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-reference.md) * [Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/repeat-expansions.md) * [De Novo Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) * [Targeted Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller.md) * [CYP2B6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) * [CYP2D6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) * [CYP21A2 Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) * [GBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/gba-calling.md) * [HBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/hba-calling.md) * [LPA Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/lpa-calling.md) * [Rh Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/rh-calling.md) * [SMN Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/smn-calling.md) * [Structural Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling.md) * [Structural Variant De Novo Quality Scoring](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) * [Structural Variant IGV Tutorial](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling/sv-igv-tutorial.md) * [Population Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/iterative-gvcf-genotyper.md) * [Filter Duplicate Variants](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/variant-deduplication.md) * [Ploidy Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling.md) * [Ploidy Estimator](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) * [Ploidy Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) * [Multi Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/multi-caller.md) * [HLA Typing](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/hla-typing.md) * [Biomarkers](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers.md) * [Tumor Mutational Burden](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) * [Microsatellite Instability](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-msi.md) * [Homologous Recombination Deficiency](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) * [Mutational Signatures](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-mutational-signatures.md) * [BRCA Large Genomic Rearrangement](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) * [DRAGEN Fragmentomics](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) * [Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/downsampling.md) * [Fractional (Raw Reads) Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/downsampling/fractional-downsampler.md) * [Unique Molecular Identifiers](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/unique-molecular-identifiers.md) * [Indel Re-aligner (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/indel-realigner.md) * [Star Allele Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/star-allele-caller.md) * [High Coverage Analysis](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/high-coverage.md) * [Population Haplotyping](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/population-haplotyping.md) * [DUX4 Rearrangement Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/dux4-rearrangement-caller.md) * [Oncovirus Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/oncovirus-detection.md) * [DRAGEN RNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline.md) * [RNA Alignment](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/rna-alignment.md) * [Gene Fusion Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/gene-fusion-detection.md) * [Gene Expression Quantification](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/gene-expression-quantification.md) * [RNA Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/rna-variant-calling.md) * [Splice Variant Caller](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/splice-variant-caller.md) * [DRAGEN Single Cell Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline.md) * [Illumina PIPseq scRNA](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-illumina.md) * [Other scRNA Prep](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-other.md) * [scATAC](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scatac.md) * [Single-Cell Multiomics](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-multiomics.md) * [Illumina TruPath Genome Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-trupath-pipeline.md) * [DRAGEN Methylation Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-methylation-pipeline.md) * [Bisulfite and TAPS Methylation Prep](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-methylation-pipeline/dragen-methylation-pipeline.md) * [DRAGEN 5-Base Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-5-base.md) * [Illumina 5-base Prep](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-5-base/dragen-5base-pipeline.md) * [DRAGEN MRD Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/mrd.md) * [DRAGEN Amplicon Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-amplicon-pipeline.md) * [DRAGEN 16S Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline.md) * [16S Pipeline Pre-Built Database](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/dragen-16s-db.md) * [16S Custom Database](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/dragen-16s-custom-db.md) * [16S Sample JSON](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/report-json-format.md) * [DRAGEN K-mer Classifier](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier.md) * [Prebuilt K-mer Databases](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/prebuilt-kmer-dbs.md) * [K-mer Classifier Database Builder](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/kmer-class-db-builder.md) * [Microbial Binner Database](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/microbial-binner.md) * [DRAGEN Microbial Enrichment Plus](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview.md) * [Reference Databases](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-databases.md) * [Custom Database](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-custom-database.md) * [Output](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-output.md) * [BCL conversion](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/bcl-conversion.md) * [DRAGEN QC Metrics](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting.md) * [Minimal Checklist](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/minimal_checklist.md) * [Contamination Detection](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/contamination-detection.md) * [FastQC](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/dragen-fastqc.md) * [CheckFingerprint](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/checkfingerprint.md) * [JSON Metrics Reporting](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/json-metrics-reporting.md) * [Illumina Connected Annotations](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/nirvana.md) * [ORA Compression](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/ora-compression.md) * [Command Line Options](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/command-line-options.md) * [Docker Requirements](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/command-line-options/docker-requirements.md) * [DRAGEN Reports](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-reports.md) * [Tools and Utilities](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/tools-and-utilities.md) * [DRAGEN Server](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/platform-maintenance.md) * [DRAGEN Multi-Cloud](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud.md) * [DRAGEN on AWS](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-aws.md) * [DRAGEN on AWS Batch](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-aws-batch.md) * [DRAGEN on Microsoft Azure](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-azure.md) * [Run DRAGEN VM on Azure](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) * [DRAGEN on Microsoft Azure Batch](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/azure-batch.md) * [Azure Batch Run Modes](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) * [DRAGEN Pricing and Licensing](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/licensing.md) * [DRAGEN OnPrem Server Licensing](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/licensing/onprem_licensing.md) * [DRAGEN Cloud FPGA BYOL](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/licensing/cloud_licensing.md) * [Support](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/technical-assistance.md) * [Resource Files](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/resource-files.md) * [Noise Baselines](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/resource-files/prebuilt-baseline-files.md) * [Supplementary Information](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/additional-resources.md) * [DRAGEN Product Obsolescence Notices](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/eol-transition.md) * [F2 Validation](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/f2-validation.md) * [Troubleshooting](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/troubleshooting.md) * [Citing DRAGEN software](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/citing-dragen.md) * [DRAGEN Publications](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/dragen-publications.md) * [Release Notes](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/release-notes-readme.md) * [DRAGEN v4.5.4 Release Notes](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/release-notes-readme/dragen-crn-v4.5.4.md) * [Revision History](https://help.connected.illumina.com/dragen/dragen-v4.5/reference/revision-history.md) - [Illumina® DRAGEN™ Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/overview/welcome-page.md) - [DRAGEN Applications](https://help.connected.illumina.com/dragen/dragen-v4.4/overview/key-applications.md) - [Deployment Options](https://help.connected.illumina.com/dragen/dragen-v4.4/overview/deployment-options.md) - [DRAGEN v4.4](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4.md) - [Getting Started](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/getting-started.md) - [DRAGEN Host Software](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software.md) - [DRAGEN Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software/dragen-platform.md) - [Clinical Research Workflows](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps.md) - [Common Product Features](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common.md) - [Sample Sheets](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/sample-sheet-introduction.md) - [Run Planning](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning.md) - [Sample Sheet Creation in BaseSpace](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/basespace-run-planning-tool.md) - [Custom Config Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/custom_config.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server.md) - [Advanced Topics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced.md) - [Data Management](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/data-storage.md) - [Illumina Connected Insights Local](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/ici-on-prem.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud.md) - [Variant Interpretation with Illumina Connected Insights](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud/ici-setup.md) - [DRAGEN Heme WGS Tumor Only Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline.md) - [Quick Start](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation.md) - [Launching Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced.md) - [Custom Config Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup.md) - [Launching Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md) - [ICA Specific Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced.md) - [Custom Workflow](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/workflow.md) - [Custom Config Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md) - [Post Processing](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/post-processing.md) - [Analysis Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-output.md) - [Analysis Methods](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/troubleshooting.md) - [DRAGEN Solid WGS Tumor Normal Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline.md) - [Quick Start](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation.md) - [Launching Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced.md) - [Custom Config Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup.md) - [Launching Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/launching-analysis.md) - [Advanced Topics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced.md) - [Custom Workflow](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced/workflow.md) - [Analysis Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-output.md) - [Analysis Methods](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/troubleshooting.md) - [DRAGEN Recipes](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes.md) - [DNA Germline Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel-umi.md) - [DNA Germline Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel.md) - [DNA Germline WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes-umi.md) - [DNA Germline WES](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes.md) - [DNA Germline WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs-umi.md) - [DNA Germline WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs.md) - [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) - [DNA Somatic Tumor-Normal Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) - [DNA Somatic Tumor-Normal Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) - [DNA Somatic Tumor-Normal Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) - [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) - [DNA Somatic Tumor-Normal Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) - [DNA Somatic Tumor-Only Heme WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) - [DNA Somatic Tumor-Only Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) - [DNA Somatic Tumor-Only Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) - [DNA Somatic Tumor-Only Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) - [DNA Somatic Tumor-Only Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) - [DNA Somatic Tumor-Only Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) - [DNA Somatic Tumor-Only Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) - [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) - [Illumina scRNA](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/illumina-scrna.md) - [Other scRNA prep](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/other-scrna-prep.md) - [RNA Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-panel.md) - [RNA WTS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-wts.md) - [DNA Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-amplicon.md) - [RNA Amplicon](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-amplicon.md) - [5 Base DNA Germline Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel-umi.md) - [5 Base DNA Germline Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel.md) - [5 Base DNA Germline WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs-umi.md) - [5 Base DNA Germline WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs.md) - [5 Base DNA Somatic Tumor-Normal Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-panel.md) - [5 Base DNA Somatic Tumor-Normal Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel-umi.md) - [5 Base DNA Somatic Tumor-Only Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel.md) - [5 Base DNA Somatic Tumor-Only Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs-umi.md) - [5 Base DNA Somatic Tumor-Only Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md) - [DRAGEN Reference Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support.md) - [Prepare a Reference Genome](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support/prepare-a-reference-genome.md) - [DRAGEN DNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline.md) - [DNA Mapping](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dna-map-align.md) - [Read Trimming](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/read-trimming.md) - [DRAGEN FASTQC](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dragen-fastqc.md) - [Sorting and Duplicate Marking](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sort-dupmark.md) - [Small Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling.md) - [ROH Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/roh-caller.md) - [B-Allele Frequency Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/baf-output.md) - [Somatic Mode](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) - [Pedigree Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/pedigree-analysis.md) - [De Novo Small Variant Filtering](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/filtering.md) - [Autogenerated MD5SUM for VCF Files](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) - [Force Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) - [Machine Learning for Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) - [Evidence BAM](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) - [Mosaic Detection](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) - [VCF Imputation](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) - [Multi-Region Joint Detection](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) - [Copy Number Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling.md) - [Available pipelines](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines.md) - [Germline CNV Calling (WGS/WES)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/germline-cnv-calling.md) - [Germline CNV Calling ASCN (WGS)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/germline-cnv-calling-wgs-ascn.md) - [Multisample Germline CNV Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/multisample-cnv-calling.md) - [Somatic CNV Calling ASCN (WGS)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wgs.md) - [Somatic CNV Calling WES](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wes.md) - [Somatic CNV Calling ASCN (WES)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wes-ascn.md) - [Additional documentation](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation.md) - [CNV Input](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-input.md) - [CNV Preprocessing](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-preprocessing.md) - [CNV Segmentation](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-segmentation.md) - [CNV Output](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-output.md) - [CNV ASCN module](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-ascn.md) - [CNV with SV Support](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-with-sv-support.md) - [Cytogenetics Modality](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cytogenetics-modality.md) - [Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions.md) - [De Novo Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) - [Targeted Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller.md) - [CYP2B6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) - [CYP2D6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) - [CYP21A2 Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) - [GBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/gba-calling.md) - [HBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/hba-calling.md) - [LPA Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/lpa-calling.md) - [Rh Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/rh-calling.md) - [SMN Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/smn-calling.md) - [Structural Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling.md) - [Structural Variant De Novo Quality Scoring](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) - [Structural Variant IGV Tutorial](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-igv-tutorial.md) - [VNTR Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/vntr-calling.md) - [Population Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/iterative-gvcf-genotyper.md) - [Filter Duplicate Variants](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/variant-deduplication.md) - [Ploidy Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling.md) - [Ploidy Estimator](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) - [Ploidy Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) - [Multi Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/multi-caller.md) - [QC Metrics Reporting](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/qc-metrics-reporting.md) - [JSON Metrics Reporting](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/json-metrics-reporting.md) - [HLA Typing](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/hla-typing.md) - [Biomarkers](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers.md) - [Tumor Mutational Burden](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) - [Microsatellite Instability](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-msi.md) - [Homologous Recombination Deficiency](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) - [BRCA Large Genomic Rearrangment](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) - [DRAGEN Fragmentomics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) - [Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling.md) - [Fractional (Raw Reads) Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling/fractional-downsampler.md) - [Unique Molecular Identifiers](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers.md) - [Indel Re-aligner (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/indel-realigner.md) - [Star Allele Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/star-allele-caller.md) - [High Coverage Analysis](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/high-coverage.md) - [CheckFingerprint](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/checkfingerprint.md) - [Population Haplotyping (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/population-haplotyping.md) - [DUX4 Rearrangement Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dux4-rearrangement-caller.md) - [DRAGEN RNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline.md) - [RNA Alignment](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-alignment.md) - [Gene Fusion Detection](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-fusion-detection.md) - [Gene Expression Quantification](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-expression-quantification.md) - [RNA Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-variant-calling.md) - [Splice Variant Caller](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/splice-variant-caller.md) - [DRAGEN Single Cell Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline.md) - [Illumina PIPseq scRNA](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna-pipseq.md) - [Other scRNA Prep](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna.md) - [scATAC](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scatac.md) - [Single-Cell Multiomics](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-multiomics.md) - [DRAGEN Methylation Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline.md) - [Illumina 5-base Prep](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline.md) - [Other Methylation Prep](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-methylation-pipeline.md) - [DRAGEN MRD Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/mrd.md) - [DRAGEN Amplicon Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-amplicon-pipeline.md) - [DRAGEN 16S Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline.md) - [16S Pipeline Pre-Built Database](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-db.md) - [16S Custom Database](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-custom-db.md) - [16S Sample JSON](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/report-json-format.md) - [Explify Analysis Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/pipeline.md) - [Kmer Classifier](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-classifier.md) - [Kmer Classifier Database Builder](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-class-db-builder.md) - [BCL conversion](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/bcl-conversion.md) - [Illumina Connected Annotations](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/nirvana.md) - [ORA Compression](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/ora-compression.md) - [Command Line Options](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/command-line-options.md) - [Docker Requirements](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/command-line-options/docker-requirements.md) - [DRAGEN Reports](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/dragen-reports.md) - [Tools and Utilities](https://help.connected.illumina.com/dragen/dragen-v4.4/product-guide/dragen-v4.4/tools-and-utilities.md) - [DRAGEN Server](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/platform-maintenance.md) - [DRAGEN Application Manager](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-application-manager.md) - [DRAGEN Multi-Cloud](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud.md) - [DRAGEN on AWS](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-aws.md) - [DRAGEN on AWS Batch](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-aws-batch.md) - [DRAGEN on Microsoft Azure](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-azure.md) - [Run DRAGEN VM on Azure](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) - [DRAGEN on Microsoft Azure Batch](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/azure-batch.md) - [Azure Batch Run Modes](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) - [DRAGEN Licensing](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/licensing.md) - [DRAGEN Server Licensing](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/licensing/onprem_licensing.md) - [DRAGEN Cloud Licensing](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/licensing/cloud_licensing.md) - [Support](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/technical-assistance.md) - [Resource Files](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/resource-files.md) - [Noise Baselines](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/resource-files/prebuilt-baseline-files.md) - [Supplementary Information](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/additional-resources.md) - [DRAGEN Product Obsolescence Notices](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/eol-transition.md) - [F2 Validation](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/f2-validation.md) - [Troubleshooting](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/troubleshooting.md) - [Citing DRAGEN software](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/citing-dragen.md) - [DRAGEN Publications](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/dragen-publications.md) - [Release Notes](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/release-notes-readme.md) - [Revision History](https://help.connected.illumina.com/dragen/dragen-v4.4/reference/revision-history.md) * [Illumina® DRAGEN™ Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.3/overview/welcome-page.md) * [DRAGEN Applications](https://help.connected.illumina.com/dragen/dragen-v4.3/overview/key-applications.md) * [Deployment Options](https://help.connected.illumina.com/dragen/dragen-v4.3/overview/deployment-options.md) * [DRAGEN v4.3](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3.md) * [Getting Started](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/getting-started.md) * [DRAGEN Host Software](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-host-software.md) * [DRAGEN Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-host-software/dragen-platform.md) * [DRAGEN Reference Support](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-reference-support.md) * [Prepare a Reference Genome](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-reference-support/prepare-a-reference-genome.md) * [DRAGEN DNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline.md) * [DNA Mapping](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dna-map-align.md) * [Read Trimming](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/read-trimming.md) * [DRAGEN FASTQC](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dragen-fastqc.md) * [Sorting and Duplicate Marking](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sort-dupmark.md) * [Small Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling.md) * [ROH Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/roh-caller.md) * [B-Allele Frequency Output](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/baf-output.md) * [Somatic Mode](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) * [Joint Analysis](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/joint-analysis.md) * [De Novo Small Variant Filtering](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/filtering.md) * [Autogenerated MD5SUM for VCF Files](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) * [Force Genotyping](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) * [Machine Learning for Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) * [Evidence BAM](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) * [Mosaic Detection](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) * [VCF Imputation](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) * [Multi-Region Joint Detection](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) * [Copy Number Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling.md) * [CNV Output](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/cnv-output.md) * [CNV with SV Support](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/cnv-with-sv-support.md) * [Multisample CNV Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/multisample-cnv-calling.md) * [Somatic CNV Calling WGS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wgs.md) * [Somatic CNV Calling WES](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wes.md) * [Allele Specific CNV for Somatic WES CNV](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wes-ascn.md) * [Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/repeat-expansions.md) * [De Novo Repeat Expansion Detection](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) * [Targeted Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller.md) * [CYPDB6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) * [CYP2D6 Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) * [CYP21A2 Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) * [GBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/gba-calling.md) * [HBA Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/hba-calling.md) * [LPA Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/lpa-calling.md) * [Rh Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/rh-calling.md) * [SMN Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/smn-calling.md) * [Structural Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sv-calling.md) * [Structural Variant De Novo Quality Scoring](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) * [VNTR Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/vntr-calling.md) * [Filter Duplicate Variants](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/variant-deduplication.md) * [Ploidy Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling.md) * [Ploidy Estimator](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) * [Ploidy Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) * [Multi Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/multi-caller.md) * [QC Metrics Reporting](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/qc-metrics-reporting.md) * [HLA Typing](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/hla-typing.md) * [Biomarkers](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers.md) * [Tumor Mutational Burden](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) * [Microsatellite Instability](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-msi.md) * [Homologous Recombination Deficiency](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) * [BRCA Large Genomic Rearrangment](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) * [DRAGEN Fragmentomics](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) * [Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling.md) * [Fractional (Raw Reads) Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling/fractional-downsampler.md) * [Effective Coverage Downsampling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling/downsampling.md) * [Unique Molecular Identifiers](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/unique-molecular-identifiers.md) * [Indel Re-aligner (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/indel-realigner.md) * [Star Allele Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/star-allele-caller.md) * [High Coverage Analysis](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/high-coverage.md) * [CheckFingerprint](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/checkfingerprint.md) * [Population Haplotyping (Beta)](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/population-haplotyping.md) * [DUX4 Rearrangement Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dux4-rearrangement-caller.md) * [DRAGEN RNA Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline.md) * [RNA Alignment](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/rna-alignment.md) * [Gene Fusion Detection](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/gene-fusion-detection.md) * [Gene Expression Quantification](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/gene-expression-quantification.md) * [RNA Variant Calling](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/rna-variant-calling.md) * [Splice Variant Caller](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/splice-variant-caller.md) * [DRAGEN Single-Cell Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline.md) * [scRNA](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-scrna.md) * [scATAC](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-scatac.md) * [Single-Cell Multiomics](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-multiomics.md) * [DRAGEN Methylation Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-methylation-pipeline.md) * [DRAGEN Amplicon Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-amplicon-pipeline.md) * [Explify Analysis Pipeline](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/pipeline.md) * [Kmer Classifier](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/pipeline/kmer-classifier.md) * [Kmer Classifier Database Builder](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/pipeline/kmer-class-db-builder.md) * [DRAGEN Recipes](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes.md) * [DNA Germline Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-panel-umi.md) * [DNA Germline Panel](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-panel.md) * [DNA Germline WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wes-umi.md) * [DNA Germline WES](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wes.md) * [DNA Germline WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wgs-umi.md) * [DNA Germline WGS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wgs.md) * [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) * [DNA Somatic Tumor-Normal Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) * [DNA Somatic Tumor-Normal Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) * [DNA Somatic Tumor-Normal Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) * [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) * [DNA Somatic Tumor-Normal Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) * [DNA Somatic Tumor-Only Heme WGS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) * [DNA Somatic Tumor-Only Solid Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) * [DNA Somatic Tumor-Only Solid Panel](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) * [DNA Somatic Tumor-Only Solid WES UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) * [DNA Somatic Tumor-Only Solid WES](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) * [DNA Somatic Tumor-Only Solid WGS UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) * [DNA Somatic Tumor-Only Solid WGS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) * [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) * [RNA Panel](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/rna-panel.md) * [RNA WTS](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/rna-wts.md) * [BCL conversion](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/bcl-conversion.md) * [Illumina Connected Annotations](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/nirvana.md) * [ORA Compression](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/ora-compression.md) * [Command Line Options](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/command-line-options.md) * [DRAGEN Reports](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/dragen-reports.md) * [Tools and Utilities](https://help.connected.illumina.com/dragen/dragen-v4.3/product-guide/dragen-v4.3/tools-and-utilities.md) * [DRAGEN Server](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/platform-maintenance.md) * [DRAGEN Multi-Cloud](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud.md) * [DRAGEN on AWS](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-aws.md) * [DRAGEN on AWS Batch](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-aws-batch.md) * [DRAGEN on Microsoft Azure](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-azure.md) * [Run DRAGEN VM on Azure](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) * [DRAGEN on Microsoft Azure Batch](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/azure-batch.md) * [Azure Batch Run Modes](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) * [DRAGEN Licensing](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/licensing.md) * [DRAGEN Server Licensing](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/licensing/onprem_licensing.md) * [DRAGEN Cloud Licensing](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/licensing/cloud_licensing.md) * [Support](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/technical-assistance.md) * [Resource Files](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/resource-files.md) * [Noise Baselines](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/resource-files/prebuilt-baseline-files.md) * [Supplementary Information](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/additional-resources.md) * [DRAGEN Product Obsolescence Notices](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/eol-transition.md) * [F2 Validation](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/f2-validation.md) * [Troubleshooting](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/troubleshooting.md) * [Citing DRAGEN software](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/citing-dragen.md) * [DRAGEN Publications](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/dragen-publications.md) * [Release Notes](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/release-notes-readme.md) * [Revision History](https://help.connected.illumina.com/dragen/dragen-v4.3/reference/revision-history.md) - [Illumina® DRAGEN™ Secondary Analysis](https://help.connected.illumina.com/dragen/dragen-v4.5-trupath/overview/welcome-page.md) - [DRAGEN v4.5](https://help.connected.illumina.com/dragen/dragen-v4.5-trupath/product-guides/dragen-v4.5.md) - [Illumina TruPath Genome Prep](https://help.connected.illumina.com/dragen/dragen-v4.5-trupath/product-guides/dragen-v4.5/dragen-trupath-pipeline.md) - [Illumina TruPath Genome WGS Recipe](https://help.connected.illumina.com/dragen/dragen-v4.5-trupath/product-guides/dragen-v4.5/illumina-trupath-genome-wgs.md) ## DRAGEN Array - [Welcome to DRAGEN Array](https://help.connected.illumina.com/dragen-array/overview/readme.md) - [DRAGEN Array Applications](https://help.connected.illumina.com/dragen-array/overview/our-features.md) - [DRAGEN Array Cloud Analysis](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis.md) - [Analysis Type Details](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview.md) - [DRAGEN Array Cytogenetics Analysis](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview/dragen-array-cytogenetics-analysis.md) - [DRAGEN Array Genotyping](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview/dragen-array-genotyping.md) - [DRAGEN Array Methylation QC](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview/dragen-array-methylation-qc.md) - [DRAGEN Array PGx CNV Calling](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview/dragen-array-pgx-cnv-calling.md) - [DRAGEN Array PGx Star Allele Annotation](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview/dragen-array-pgx-star-allele.md) - [BaseSpace](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1.md) - [Manage Data](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1/manage-data.md) - [Launch Analysis](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1/launch-analysis.md) - [Plan Analysis](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1/plan-analysis.md) - [Share Project](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1/share-project.md) - [Troubleshoot iScan Integration](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis/overview-1/troubleshoot-iscan.md) - [DRAGEN Array Local Analysis](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-local-analysis.md) - [Input Files](https://help.connected.illumina.com/dragen-array/product-guides/input-files.md) - [Output Files](https://help.connected.illumina.com/dragen-array/product-guides/output-files.md) - [Support and Additional Resources](https://help.connected.illumina.com/dragen-array/reference/support-and-additional-resources.md) - [Frequently Asked Questions](https://help.connected.illumina.com/dragen-array/reference/faq.md) - [Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes.md) - [DRAGEN Array v1.3.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.3.0-release-notes.md) - [DRAGEN Array v1.3.0 + Emedgene V100.39.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.3.0-release-notes/dragen-array-v1.3.0-emg-release-notes.md) - [DRAGEN Array v1.2.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.2.0-release-notes.md) - [DRAGEN Array v1.2.0 Emedgene V38.0 Automatic Case Creation Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.2.0-release-notes/dragen-array-v1.2.0-cyto-emg-release-notes.md) - [DRAGEN Array v1.1.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.1.0-release-notes.md) - [DRAGEN Array Methylation QC Cloud v1.0.1 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.0.1-cloud-methylqc-release-notes.md) - [DRAGEN Array v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.0.0-release-notes.md) - [DRAGEN Array Genotyping Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-genotype-release-notes.md) - [DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-methylqc-release-notes.md) - [PGx CNV Coverage](https://help.connected.illumina.com/dragen-array/reference/pgx-cnv-coverage.md) - [PGx Allele Definitions and PGx Guidelines](https://help.connected.illumina.com/dragen-array/reference/pgx-allele-definitions-and-pgx-guidelines.md) - [PGx Star Allele Coverage](https://help.connected.illumina.com/dragen-array/reference/pgx-star-allele-coverage.md) - [Document Revision History](https://help.connected.illumina.com/dragen-array/reference/document-revision-history.md) * [Welcome to DRAGEN Array](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/overview/readme.md) * [DRAGEN Array Applications](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/overview/our-features.md) * [DRAGEN Array Cloud Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/product-guides/dragen-array-cloud-analysis.md) * [DRAGEN Array Local Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/product-guides/dragen-array-local-analysis.md) * [Input Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/product-guides/input-files.md) * [Output Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/product-guides/output-files.md) * [Support and Additional Resources](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/support-and-additional-resources.md) * [Frequently Asked Questions](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/faq.md) * [Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes.md) * [DRAGEN Array v1.2.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.2.0-release-notes.md) * [DRAGEN Array v1.2.0 EMGv38 Automatic Case Creation Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.2.0-release-notes/dragen-array-v1.2.0-cyto-emg-release-notes.md) * [DRAGEN Array v1.1.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.1.0-release-notes.md) * [DRAGEN Array v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.0.0-release-notes.md) * [DRAGEN Array Genotyping Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-genotype-release-notes.md) * [DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-methylqc-release-notes.md) * [PGx CNV Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/pgx-cnv-coverage.md) * [PGx Allele Definitions and PGx Guidelines](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/pgx-allele-definitions-and-pgx-guidelines.md) * [PGx Star Allele Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/pgx-star-allele-coverage.md) * [Document Revision History](https://help.connected.illumina.com/dragen-array/dragen-array-v1.2/reference/document-revision-history.md) - [Welcome to DRAGEN Array](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/overview/readme.md) - [DRAGEN Array Applications](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/overview/our-features.md) - [DRAGEN Array Cloud Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/product-guides/dragen-array-cloud-analysis.md) - [DRAGEN Array Local Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/product-guides/dragen-array-local-analysis.md) - [Input Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/product-guides/input-files.md) - [Output Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/product-guides/output-files.md) - [Support and Additional Resources](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/support-and-additional-resources.md) - [Frequently Asked Questions](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/faq.md) - [Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/release-notes.md) - [DRAGEN Array v1.1.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/release-notes/dragen-array-v1.1.0-release-notes.md) - [DRAGEN Array v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/release-notes/dragen-array-v1.0.0-release-notes.md) - [DRAGEN Array Genotyping Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-genotype-release-notes.md) - [DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-methylqc-release-notes.md) - [PGx CNV Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/pgx-cnv-coverage.md) - [PGx Allele Definitions and PGx Guidelines](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/pgx-allele-definitions-and-pgx-guidelines.md) - [PGx Star Allele Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/pgx-star-allele-coverage.md) - [Document Revision History](https://help.connected.illumina.com/dragen-array/dragen-array-v1.1/reference/document-revision-history.md) * [Welcome to DRAGEN Array](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/overview/readme.md) * [DRAGEN Array Applications](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/overview/our-features.md) * [DRAGEN Array Cloud Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/dragen-array-cloud-analysis.md) * [DRAGEN Array Local Analysis](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/dragen-array-local-analysis.md) * [Input Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/input-files.md) * [Output Files](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/output-files.md) * [Support and Additional Resources](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/support-and-additional-resources.md) * [Frequently Asked Questions](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/faq.md) * [Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/release-notes.md) * [DRAGEN Array v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/release-notes/dragen-array-v1.0.0-release-notes.md) * [DRAGEN Array Genotyping Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-genotype-release-notes.md) * [DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/release-notes/dragen-array-v1.0.0-release-notes/dragen-array-v1.0.0-cloud-methylqc-release-notes.md) * [PGx CNV Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/pgx-cnv-coverage.md) * [PGx Allele Definitions and PGx Guidelines](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/pgx-allele-definitions-and-pgx-guidelines.md) * [PGx Star Allele Coverage](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/pgx-star-allele-coverage.md) * [Document Revision History](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/reference/document-revision-history.md) ## DRAGEN Clinical Research Apps - [Clinical Research Workflows](https://help.connected.illumina.com/dragen-clinical-research-apps/readme.md) - [Common Product Features](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common.md) - [Sample Sheets](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/sample-sheet-introduction.md) - [Run Planning](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/run-planning.md) - [Sample Sheet Creation in BaseSpace](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/run-planning/basespace-run-planning-tool.md) - [Custom Config Support](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/run-planning/custom_config.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/server.md) - [Advanced Topics](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/server/advanced.md) - [Data Management](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/server/advanced/data-storage.md) - [Illumina Connected Insights Local](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/server/advanced/ici-on-prem.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/cloud.md) - [Variant Interpretation with Illumina Connected Insights](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/cloud/ici-setup.md) - [Post Processing](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/common/cloud/post-processing.md) - [DRAGEN Heme WGS Tumor Only Pipeline](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline.md) - [Quick Start](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation.md) - [Launching Analysis](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/advanced.md) - [Custom Config Support](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup.md) - [Launching Analysis](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md) - [ICA Specific Output](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/advanced.md) - [Custom Workflow](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/advanced/workflow.md) - [Custom Config Support](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md) - [Analysis Output](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/analysis-output.md) - [Analysis Methods](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/troubleshooting.md) - [DRAGEN Solid WGS Tumor Normal Pipeline](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline.md) - [Quick Start](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation.md) - [Launching Analysis](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/advanced.md) - [Custom Config Support](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/setup.md) - [Launching Analysis](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/setup/launching-analysis.md) - [Advanced Topics](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/setup/advanced.md) - [Custom Config Support](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/setup/advanced/custom_config.md) - [Analysis Output](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/analysis-output.md) - [Analysis Methods](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/troubleshooting.md) ## DRAGEN ORA - [Illumina® DRAGEN™ ORA Decompression Software Family](https://help.connected.illumina.com/ora/introduction/readme.md) - [DRAGEN ORA Decompression v2.7](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression.md) - [Software Installation](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression/software-installation.md) - [References Installation](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression/references-installation.md) - [Commands](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression/commands.md) - [Combine with downstream analysis](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression/commands/with-downstream-analysis.md) - [Check Losslessness](https://help.connected.illumina.com/ora/product-guides/dragen-ora-decompression/commands/check-losslessness.md) - [DRAGEN ORA Helper Suite v2.0](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite.md) - [Remote and Local Usage](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/usage.md) - [Installation Software and References](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/installation.md) - [Commands for the ORA Helper Suite software](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/tools.md) - [Commands for Interleaved fastq.ora files](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/interleaved-files.md) - [Handling of fastq.ora files compressed with reference other than default human reference](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/files-compressed-with-other-reference.md) - [Troubleshooting](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/troubleshooting.md) - [Supported References](https://help.connected.illumina.com/ora/reference/supported-references.md) - [Resources](https://help.connected.illumina.com/ora/reference/resources.md) - [Terms](https://help.connected.illumina.com/ora/reference/disclaimer.md) - [Revision History](https://help.connected.illumina.com/ora/reference/revision.md) ## DRAGEN Somatic for IDT Custom Panels - [Introduction](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/readme.md) - [About DRAGEN somatic for IDT Custom Panels](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/get-started/about.md) - [Prerequisites](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/get-started/prerequisites.md) - [Workflow Overview](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/workflow/workflow.md) - [Choose Your Entry Point](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/workflow/entry-points.md) - [Why Systematic Noise Matters](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/noise-baseline.md) - [Option A: From Run Planner](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/option-a-run-planner.md) - [Option B: From BSSH](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/option-b-bssh-ica.md) - [Option C: Pre-Built Reference Files](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/option-c-prebuilt.md) - [Inputs and Modes](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/variant-calling.md) - [Low-Quality FFPE Mode](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md) - [Option A: Launch from Run Planner](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-a-run-planner.md) - [Option B: Launch from BSSH](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-b-bssh-ica.md) - [Where to Find Your Results](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/review-outputs/find-results.md) - [Output Files](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/review-outputs/outputs.md) - [Key VCF Fields](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/review-outputs/vcf-fields.md) - [Key QC Metrics](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/qc-and-interpretation/qc.md) - [Connecting to Connected Insights](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/qc-and-interpretation/connected-insights.md) - [Analysis Failed to Launch](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/troubleshooting/launch-failures.md) - [Missed Variant Calls](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/troubleshooting/missed-variants.md) - [Unexpected Variant Calls](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/troubleshooting/false-positives.md) - [Pricing](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/reference/pricing.md) ## Illumina Connected Analytics - [Introduction](https://help.connected.illumina.com/connected-analytics/readme.md) - [About the Platform](https://help.connected.illumina.com/connected-analytics/get-started/gs-abouttheplatform.md) - [Get Started](https://help.connected.illumina.com/connected-analytics/get-started/gs-getstarted.md) - [Projects](https://help.connected.illumina.com/connected-analytics/home/h-projects.md) - [Bundles](https://help.connected.illumina.com/connected-analytics/home/h-bundles.md) - [Event Log](https://help.connected.illumina.com/connected-analytics/home/h-eventlog.md) - [Metadata Models](https://help.connected.illumina.com/connected-analytics/home/h-metadatamodels.md) - [Docker Repository](https://help.connected.illumina.com/connected-analytics/home/h-dockerrepository.md) - [Tool Repository](https://help.connected.illumina.com/connected-analytics/home/h-toolrepository.md) - [Storage](https://help.connected.illumina.com/connected-analytics/home/h-storage.md) - [Connect AWS S3 Bucket](https://help.connected.illumina.com/connected-analytics/home/h-storage/s-awss3.md) - [IAM User Method](https://help.connected.illumina.com/connected-analytics/home/h-storage/s-awss3/iam-user-method.md) - [IAM Role Method](https://help.connected.illumina.com/connected-analytics/home/h-storage/s-awss3/iam-role-method.md) - [SSE-KMS Encryption](https://help.connected.illumina.com/connected-analytics/home/h-storage/s-awss3/s-sse-kms.md) - [Troubleshooting AWS-S3 Connectivity](https://help.connected.illumina.com/connected-analytics/home/h-storage/s-awss3/troubleshooting-aws-s3-connectivity.md) - [Data](https://help.connected.illumina.com/connected-analytics/project/p-data.md) - [Non-Indexed Folders](https://help.connected.illumina.com/connected-analytics/project/p-data/non-indexed-folders.md) - [Data Integrity](https://help.connected.illumina.com/connected-analytics/project/p-data/data-integrity.md) - [Storage Cost Managment](https://help.connected.illumina.com/connected-analytics/project/p-data/storage-cost-managment.md) - [Data - Troubleshooting](https://help.connected.illumina.com/connected-analytics/project/p-data/data-troubleshooting.md) - [Samples](https://help.connected.illumina.com/connected-analytics/project/p-samples.md) - [Activity](https://help.connected.illumina.com/connected-analytics/project/p-activity.md) - [Flow](https://help.connected.illumina.com/connected-analytics/project/p-flow.md) - [Reference Data](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-referencedata.md) - [Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines.md) - [Nextflow](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-nextflow.md) - [CWL](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-cwl.md) - [XML Input Form](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-inputform.md) - [JSON-Based input forms](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms.md) - [inputForm.json](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/inputform-json.md) - [JSON Schema](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/inputform-json/inputform.json-syntax.md) - [onRender.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onrender.js.md) - [onSubmit.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onsubmit.js.md) - [onFinished.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onfinished.js.md) - [JSON Scatter Gather Pipeline](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/json-scatter-gather-pipeline.md) - [Git-Sourced Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/git-sourced-pipelines-experimental.md) - [Basic Git-Sourced Pipeline Example](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/git-sourced-pipelines-experimental/basic-git-sourced-pipeline-example.md) - [Tips and Tricks](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-tips.md) - [Analyses](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-analyses.md) - [Base](https://help.connected.illumina.com/connected-analytics/project/p-base.md) - [Tables](https://help.connected.illumina.com/connected-analytics/project/p-base/base-tables.md) - [Data Catalogue](https://help.connected.illumina.com/connected-analytics/project/p-base/base-tables/datacatalogue.md) - [Query](https://help.connected.illumina.com/connected-analytics/project/p-base/base-query.md) - [Schedule](https://help.connected.illumina.com/connected-analytics/project/p-base/base-schedule.md) - [Snowflake](https://help.connected.illumina.com/connected-analytics/project/p-base/base-snowflake.md) - [Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench.md) - [Workspaces](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces.md) - [Bench Clusters](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/bench-clusters.md) - [Sun Grid Engine (SGE) on ICA Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/sun-grid-engine-sge-on-ica-bench.md) - [Spark on ICA Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/spark-on-ica-bench.md): Running a Spark application in a Bench Spark Cluster - [JupyterLab](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-jupyterlab.md) - [Bring Your Own Bench Image](https://help.connected.illumina.com/connected-analytics/project/p-bench/bring-your-own-bench-image.md) - [Bench Command Line Interface](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-command-line-interface.md) - [Pipeline Development in Bench (Experimental)](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental.md) - [Creating a Pipeline from Scratch](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/creating-a-pipeline-from-scratch.md) - [nf-core Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/nf-core-pipelines.md) - [Updating an Existing Flow Pipeline](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/updating-an-existing-flow-pipeline.md) - [Containers in Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/containers-in-bench.md) - [FUSE Driver](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-fusedriver.md) - [Run DRAGEN in Bench - Interactive](https://help.connected.illumina.com/connected-analytics/project/p-bench/run-dragen-in-bench-interactive.md) - [Cohorts](https://help.connected.illumina.com/connected-analytics/project/p-cohorts.md) - [Create a Cohort](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-create.md) - [Import New Samples](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-import.md) - [Prepare Metadata Sheets](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-metadata.md) - [Precomputed GWAS and PheWAS](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-gwas-phewas.md) - [Cohort Analysis](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-analysis.md) - [Compare Cohorts](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-comparison.md) - [Cohorts Data in ICA Base](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-base.md) - [Oncology Walk-through](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-walkthrough-cancer.md) - [Rare Genetic Disorders Walk-through](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-walkthrough-raredisease.md) - [Public Data Sets](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-publicdata.md) - [Details](https://help.connected.illumina.com/connected-analytics/project/p-details.md) - [Team](https://help.connected.illumina.com/connected-analytics/project/p-team.md) - [Connectivity](https://help.connected.illumina.com/connected-analytics/project/p-connectivity.md) - [Service Connector](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/service-connector.md) - [Service Connector Troubleshooting](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/service-connector/service-connector-troubleshooting.md) - [Project Connector](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/project-connector.md) - [Notifications](https://help.connected.illumina.com/connected-analytics/project/p-notifications.md) - [Installation](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-installation.md) - [Authentication](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-authentication.md) - [Data Transfer](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-datatransfer.md) - [Config Settings](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-configsettings.md) - [Output Format](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-outputformat.md) - [Command Index](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-indexcommands.md) - [Releases](https://help.connected.illumina.com/connected-analytics/command-line-interface/cli-releasehistory.md) - [Cloud Analysis Auto-launch](https://help.connected.illumina.com/connected-analytics/sequencer-integration/analysis_autolaunch.md) - [Nextflow Pipeline](https://help.connected.illumina.com/connected-analytics/tutorials/nextflow.md) - [Nextflow DRAGEN Pipeline](https://help.connected.illumina.com/connected-analytics/tutorials/nextflow/nextflow-dragen-pipeline.md) - [Nextflow: Scatter-gather Method](https://help.connected.illumina.com/connected-analytics/tutorials/nextflow/scatter-gather-nextflow.md) - [Nextflow: Pipeline Lift](https://help.connected.illumina.com/connected-analytics/tutorials/nextflow/nextflow_pipeline_liftovers.md) - [Nextflow CLI](https://help.connected.illumina.com/connected-analytics/tutorials/nextflow/nextflow-cli-tutorial.md) - [CWL CLI Pipeline Execution](https://help.connected.illumina.com/connected-analytics/tutorials/cli-cwl.md) - [CWL Graphical Pipeline](https://help.connected.illumina.com/connected-analytics/tutorials/cli-cwl/cwl-graphical-pipeline.md) - [CWL DRAGEN Pipeline](https://help.connected.illumina.com/connected-analytics/tutorials/cli-cwl/cwl-dragen-pipeline.md) - [CWL: Scatter-gather Method](https://help.connected.illumina.com/connected-analytics/tutorials/cli-cwl/scatter-gather.md) - [Base Basics](https://help.connected.illumina.com/connected-analytics/tutorials/base_basics.md) - [Base: SnowSQL](https://help.connected.illumina.com/connected-analytics/tutorials/base_basics/base_snowsql.md) - [Base: Access Tables via Python](https://help.connected.illumina.com/connected-analytics/tutorials/base_basics/dashboard.md) - [Bench ICA Python Library](https://help.connected.illumina.com/connected-analytics/tutorials/bench-ica-python-library.md) - [API Beginner Guide](https://help.connected.illumina.com/connected-analytics/tutorials/api-introduction.md) - [Launching a DRAGEN Pipeline](https://help.connected.illumina.com/connected-analytics/tutorials/launching-a-dragen-pipeline.md) - [End-to-End User Flow: DRAGEN Analysis](https://help.connected.illumina.com/connected-analytics/tutorials/end-to-end-1.md) - [Data Transfer Options](https://help.connected.illumina.com/connected-analytics/tutorials/datatransfer.md) - [Pipeline Chaining on AWS](https://help.connected.illumina.com/connected-analytics/tutorials/pipeline_chaining_aws.md) - [Software Release Notes](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes.md) - [2026](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2026.md) - [2025](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2025.md) - [2024](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2024.md) - [2023](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2023.md) - [2022](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2022.md) - [2021](https://help.connected.illumina.com/connected-analytics/reference/software-release-notes/2021.md) - [Known Issues](https://help.connected.illumina.com/connected-analytics/reference/r-knownissues.md) - [API](https://help.connected.illumina.com/connected-analytics/reference/r-api.md) - [Pricing](https://help.connected.illumina.com/connected-analytics/reference/r-pricing.md) - [Security and Compliance](https://help.connected.illumina.com/connected-analytics/reference/r-securityandcompliance.md) - [Network Settings](https://help.connected.illumina.com/connected-analytics/reference/r-networksettings.md) - [ICA Terminology](https://help.connected.illumina.com/connected-analytics/reference/r-terms.md) - [External Resources](https://help.connected.illumina.com/connected-analytics/reference/r-resources.md) - [Data Formats](https://help.connected.illumina.com/connected-analytics/reference/r-dataformats.md) - [FAQ](https://help.connected.illumina.com/connected-analytics/reference/r-faq.md) ## Illumina FFPE DNA Prep with Exome 2.5 - [Illumina FFPE DNA Prep with Exome 2.5 Enrichment](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/readme.md) - [Demo Data](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/demo-data.md) - [Resource Files](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/resource-files.md) - [DRAGEN v4.4.6 T/N Recipe](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/tumor-normal-software-guides/dragen-v4.3.17-recipe.md) - [BaseSpace Sequence Hub (BSSH) T/N](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/tumor-normal-software-guides/page.md): Detailed instructions on how to configure the DRAGEN command-line for analyzing paired tumor-normal samples processed with the Illumina FFPE DNA Prep with Exome 2.5 Enrichment. - [Illumina Connected Analytics (ICA) T/N](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/tumor-normal-software-guides/page-2.md) - [Microsatellite Instability (MSI)](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/microsatellite-instability-msi.md): Microsatellite Instability (MSI) If MSI values are needed ahead of software updates, it is recommend to calculate MSI on the tumor fastq files in tumor-only mode in a separate DRAGEN analysis. Tumor-o - [Quick check of run quality](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/quick-check-of-run-quality.md) - [Spike-in panels](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/spike-in-panels.md) - [Germline variants](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/germline-variants.md) - [Troubleshooting the analysis](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/troubleshooting-the-analysis.md): Potential changes to the analysis settings to improve performance when analyzing Illumina FFPE DNA Prep with Exome 2.5 Enrichment. - [Tumor-only analysis](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/tumor-only-analysis.md) ## Illumina TruPath Genome - [Introduction](https://help.connected.illumina.com/illumina-trupath-genome/get-started/readme.md): Illumina TruPath Genome Software Product Overview - [Quick Start Guide](https://help.connected.illumina.com/illumina-trupath-genome/get-started/readme-1.md): This page provides high level information for installation, configuration, running, and analysis for the Illumina TruPath Genome Software Solution. - [Prerequisites](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/instrument-run-setup.md) - [NovaSeq X Instrument Domain Setup](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/novaseq-x-instrument-domain-setup.md): This page describes how to access and set up the private domain on instrument. - [NovaSeq X Run Planning - BCL Convert](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/novaseq-x-run-planning-bcl-convert.md): This page gives an overview of generating a Sample Sheet on BaseSpace for sequencing on NovaSeq X Sequencing Systems. This Sample Sheet is required for on-prem BCL Convert via DRAGEN Server. - [NovaSeq X Run Planning - DRAGEN Germline](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/novaseq-x-run-planning-dragen-germline.md): This page gives an overview of how to plan a run on BaseSpace for the NovaSeq X Series using Cloud DRAGEN Germline analysis for the Illumina TruPath Genome workflow. - [Accessing Results](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/accessing-results.md) - [Cloud Analysis Settings](https://help.connected.illumina.com/illumina-trupath-genome/run-analysis-setup/cloud-analysis-settings.md): Overview of DRAGEN Secondary Analysis and Cloud Analysis Settings - [ICA Analysis](https://help.connected.illumina.com/illumina-trupath-genome/run-analysis-setup/ica-analysis.md): This section describes the steps required to execute the DRAGEN Germline 4.5.2 analysis on Illumina Connected Analytics (ICA). - [On-Prem DRAGEN Server Analysis](https://help.connected.illumina.com/illumina-trupath-genome/run-analysis-setup/on-prem-dragen-server-analysis.md): This page describes details on running Illumina TruPath Genome analysis on prem via DRAGEN Server. - [TruPath Outputs](https://help.connected.illumina.com/illumina-trupath-genome/outputs-and-metrics/output-files-and-metrics.md): This page describes key DRAGEN secondary analysis outputs and metrics. - [TruPath Metrics](https://help.connected.illumina.com/illumina-trupath-genome/outputs-and-metrics/trupath-metrics.md): Reference guide for interpreting DRAGEN sequencing and proximity metrics and identifying potential performance issues. - [Visualize Data in IGV](https://help.connected.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-igv.md): This page provides instructions for visualizing DRAGEN secondary analysis outputs using IGV. - [Visualize Data in DRAGEN Reports](https://help.connected.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-dragen-reports.md): This page describes how to visualize Multi-Region Joint Detection (MRJD) Outputs in DRAGEN Reports. - [Visualize Data in HiGlass](https://help.connected.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-higlass.md): This page provides instructions for visualizing DRAGEN secondary analysis outputs using HiGlass. - [Tertiary Analysis](https://help.connected.illumina.com/illumina-trupath-genome/tertiary-analysis/tertiary-analysis.md): This page outlines the tertiary analysis software supporting the Illumina TruPath Genome prep. - [Known Limitations](https://help.connected.illumina.com/illumina-trupath-genome/additional-information/known-limitations.md): This page describes known limitations of the Illumina TruPath Genome software solution. - [FAQs](https://help.connected.illumina.com/illumina-trupath-genome/additional-information/faqs.md): This page describes Frequently Asked Questions (FAQs) related to Illumina TruPath Genome Software. - [Release History](https://help.connected.illumina.com/illumina-trupath-genome/additional-information/release-history.md) ## Infectious Disease and Microbiology Software - [Illumina Infectious Disease and Microbiology Software](https://help.connected.illumina.com/infectious-disease/readme.md): This page provides an overview of the software available on Illumina's cloud platforms - [DRAGEN Microbial Amplicon App Documentation](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon.md) - [How to start](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/start.md) - [Custom reference](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/custom.md) - [Reference FASTA](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/fasta.md) - [Reference BED](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/bed.md) - [PCR primer definition](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/pcr-primer-definition.md) - [Output files](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/output.md) - [Understanding the BaseSpace reports](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports.md) - [Summary](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports/summary.md) - [Sample Report](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports/sample-report.md) - [Pipeline Logic](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/pipeline.md) - [Special considerations for amplicon detection](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/amplicon-detection.md) - [Additional analysis](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/additional-analysis.md) - [Frequently asked questions (FAQ)](https://help.connected.illumina.com/infectious-disease/dragen-microbial-amplicon/dragen-microbial-amplicon/faq.md) - [DRAGEN Targeted Microbial App Documentation](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial.md) - [How to set up and run an analysis](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/setting-up-an-analysis.md) - [Custom genomes and primer sets](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets.md) - [Genome definition file formats](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets/genome-definition-file-formats.md) - [Primer definition file formats](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets/primer-definition-file-formats.md) - [App Settings](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/settings.md): Describes the controls on the Input Form and their function - [Understanding the BaseSpace Reports](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports.md): Brief description of Summary and Result reports and an explanation of their contents - [Summary Report](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports/summary-report.md): Describes the report that can be viewed from the Summary link on the Reports tab of a completed analysis. - [Result Reports](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports/result-reports.md): Describes the reports that can be viewed from the individual sample links on the left side of the reports tab or by clicking on sample names in the Metrics by sample table. - [Output files](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/output-files.md) - [Pipeline Logic](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/pipeline-logic.md): Descriptions of the logic underlying the DRAGEN Targeted Microbial analysis pipeline - [Special considerations for amplicon sequencing with IMAP protocols](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/special-considerations-for-amplicon-sequencing-with-imap-protocols.md) - [Frequently Asked Questions (FAQ)](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/frequently-asked-questions-faq.md) - [Known issues](https://help.connected.illumina.com/infectious-disease/dragen-targeted-microbial/dragen-targeted-microbial/known-issues.md) - [DRAGEN Microbial Enrichment Plus App Documentation](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus.md) - [How to set up and run an analysis](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis.md) - [Custom reference FASTA and BED files](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/custom-reference-fasta-and-bed-files.md) - [Microorganism Reporting File format](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/microorganism-reporting-file-format.md) - [Output files](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files.md) - [Understanding the BaseSpace HTML reports](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/understanding-the-basespace-html-reports.md) - [Report JSON format](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/report-json-format.md) - [Pipeline logic](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/pipeline-logic.md) - [Test information](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information.md) - [RPIP](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/rpip.md) - [UPIP](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/upip.md) - [RVOP/RVEK](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/rvop-rvek.md) - [VSP](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/vsp.md) - [VSP V2](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/vsp-v2.md) - [Custom Panel](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/custom-panel.md) - [Scientific evidence](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/scientific-evidence.md) - [Frequently Asked Questions (FAQ)](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/frequently-asked-questions-faq.md) - [Release notes](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/release-notes.md) - [DRAGEN 16S Plus App Documentation](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus.md) - [How to set up and run an analysis](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/how-to-set-up-and-run-an-analysis.md) - [Custom database FASTA file format](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/how-to-set-up-and-run-an-analysis/custom-database-fasta-file-format.md) - [Output files](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/output-files.md) - [Understanding the BaseSpace HTML reports](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/output-files/understanding-the-basespace-html-reports.md) - [Report JSON format](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/output-files/report-json-format.md) - [Pipeline logic](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/pipeline-logic.md) - [Test information](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/test-information.md) - [Frequently Asked Questions (FAQ)](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/frequently-asked-questions-faq.md) - [Release notes](https://help.connected.illumina.com/infectious-disease/dragen-16s-plus/dragen-16s-plus/release-notes.md) ## TruSight Oncology 500 - [DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software](https://help.connected.illumina.com/tso500/readme.md) - [F2 Support on ICA](https://help.connected.illumina.com/tso500/f2-support-on-ica.md) - [Performance Testing](https://help.connected.illumina.com/tso500/performance-testing.md) - [Known Limitations with Commercial Controls](https://help.connected.illumina.com/tso500/performance-testing/known-limitations-with-commercial-controls.md) - [Commercial Control Use with TSO 500 ctDNA](https://help.connected.illumina.com/tso500/performance-testing/commercial-control-use-with-tso-500-ctdna.md): The page aggregates materials to help plan analytical studies with commercial controls for TruSight Oncology ctDNA v2 assay. - [Demo Data](https://help.connected.illumina.com/tso500/performance-testing/demo-data.md) - [DRAGEN TSO 500 v2.6](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6.md) - [Introduction to DRAGEN TSO 500 Analysis Software v2.6.x](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview.md) - [Getting Started](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started.md) - [Installation of 2.6.0 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started/installation-of-2.6.0-on-standalone-dragen-server.md) - [Installation of 2.6.1 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started/installation-of-2.6.1-on-standalone-dragen-server.md) - [Installation of 2.6.2 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started/installation-of-2.6.2-on-standalone-dragen-server.md) - [Getting Started on Illumina Connected Analytics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started/requirements.md) - [Installation of NovaSeq 6000Dx TSO 500 Analysis Application](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/getting-started/installation-of-novaseq-6000dx-tso-500-analysis-application.md): Instructions to install DRAGEN TSO 500 Analysis Application on NovaSeq 6000Dx (RUO mode). - [Run Planning](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning.md) - [Sample Sheet Introduction](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/sample-sheet-introduction.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/sample-sheet-requirements.md): DRAGEN TSO 500 Analysis Software has optional and required fields that are required in addition to general sample sheet requirements. Follow the steps below to create a valid sample sheet. - [Sample Sheet Creation in BaseSpace Run Planning tool](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/sample-sheet-creation-in-basespace-run-planning-tool.md) - [Multi-Assay Flow Cells](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/multi-assay-flow-cells.md): How to plan a run and analyze data with multiple assays loaded individually per lane on one flow cell. - [NovaSeq 6000Dx Run Set Up](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/novaseq-6000dx-run-set-up.md): The following instructions describe steps to set up a run on NovaSeq 6000Dx Analysis Application. - [Sample Sheet Templates](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/run-planning/sample-sheet-templates.md): Sample Sheet templates for TSO 500 standalone DRAGEN server and ICA manual launch analysis can be found in the table below. For auto-launch compatible sample sheets, use BaseSpace Run Planner. - [Launching Analysis](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis.md) - [Input Checks](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/input-checks.md): Items to check before submitting your analysis - [Analysis Launch on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/run-dragen-tso-software.md) - [Command-Line Options](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/run-dragen-tso-software/command-line-options.md) - [Run on Multiple DRAGEN Servers](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/run-dragen-tso-software/run-on-multiple-dragen-servers.md) - [Analysis Launch on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/analysis-launch-on-ica.md) - [Auto-Launch of DRAGEN TSO 500 Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/analysis-launch-on-ica/autolaunch.md) - [Auto-Launch with FASTQs generated by Standalone BCL Convert Pipeline (Start from FASTQ)](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/analysis-launch-on-ica/autolaunch/auto-launch-with-fastqs-generated-by-standalone-bcl-convert-pipeline-start-from-fastq.md) - [Manual Launch of DRAGEN TSO 500 Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/analysis-launch-on-ica/manual-launch.md) - [Analysis Launch with NovaSeq 6000Dx Application](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/launching-analysis/analysis-launch-with-novaseq-6000dx-application.md) - [Analysis Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output.md) - [DNA Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/dna-output.md) - [HRD and GIS Outputs](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/dna-output/hrd-and-gis-outputs.md) - [RNA Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/rna-output.md) - [Combined Variant Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/combined-variant-output.md) - [Metrics Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/metrics-output.md) - [Coverage Reports](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/coverage-reports.md) - [Block List](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/analysis-output/block-list.md) - [Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1.md) - [FastQ Generation](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/fastq-generation.md) - [Quality Control](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control.md) - [Run QC](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/run-qc.md) - [Contamination](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/contamination.md) - [Sample QC](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/sample-qc.md) - [DNA Expanded Metrics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/dna-expanded-metrics.md) - [RNA Expanded Metrics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/rna-expanded-metrics.md) - [DNA Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/dna-analysis-methods.md) - [Block List](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/dna-analysis-methods/block-list.md) - [RNA Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/rna-analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting.md) - [Standalone DRAGEN Server - Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting/standalone-dragen-server-troubleshooting.md) - [ICA Pipeline Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting/ica-pipeline-troubleshooting.md) - [NovaSeq 6000Dx App Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting/novaseq-6000dx-app-troubleshooting.md) - [Sample Sheet Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting/sample-sheet-troubleshooting.md) - [Analysis Pipeline Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/troubleshooting/analysis-pipeline-troubleshooting.md) - [DRAGEN TSO 500 v2.5](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5.md) - [Introduction to DRAGEN TSO 500 Analysis Software v2.5.x](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/introduction-to-dragen-tso-500-analysis-software-v2.5.x.md) - [Getting Started](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/getting-started.md) - [Installation of 2.5.3 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/getting-started/installation-of-2.5.3-on-standalone-dragen-server.md) - [Installation of v2.5.4 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/getting-started/installation-of-v2.5.4-on-standalone-dragen-server.md) - [Getting Started on Illumina Connected Analytics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/getting-started/getting-started-on-illumina-connected-analytics.md) - [Run Planning](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/run-planning.md) - [Sample Sheet Introduction](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/run-planning/sample-sheet-introduction.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/run-planning/sample-sheet-requirements.md): DRAGEN TSO 500 Analysis Software has optional and required fields that are required in addition to general sample sheet requirements. Follow the steps below to create a valid samplesheet. - [Sample Sheet Creation in BaseSpace Run Planning tool](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/run-planning/sample-sheet-creation-in-basespace-run-planning-tool.md) - [Sample Sheet Templates](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/run-planning/sample-sheet-templates.md): Sample Sheet templates for TSO 500 v2.5.x standalone DRAGEN server and ICA manual launch analysis can be found in the table below. For auto-launch compatible sample sheets, use BaseSpace Run Planner. - [Launching Analysis](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis.md) - [Analysis Launch on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-standalone-dragen-server.md) - [Command-Line Options](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-standalone-dragen-server/command-line-options.md) - [Run on Multiple DRAGEN Servers](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-standalone-dragen-server/run-on-multiple-dragen-servers.md) - [Analysis Launch on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-ica.md) - [Auto-Launch of DRAGEN TSO 500 Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-ica/auto-launch-of-dragen-tso-500-analysis-on-ica.md) - [Manual Launch of DRAGEN TSO 500 Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/launching-analysis/analysis-launch-on-ica/manual-launch-of-dragen-tso-500-analysis-on-ica.md) - [Analysis Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output.md) - [DNA Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/dna-output.md) - [HRD and GIS Outputs](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/dna-output/hrd-and-gis-outputs.md) - [RNA Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/rna-output.md) - [Combined Variant Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/combined-variant-output.md) - [Metrics Output](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/metrics-output.md) - [Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods.md) - [FASTQ Generation](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/fastq-generation.md) - [DNA Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/dna-analysis-methods.md) - [Block List](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/dna-analysis-methods/block-list.md) - [RNA Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/rna-analysis-methods.md) - [Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/troubleshooting.md) - [DRAGEN TSO 500 ctDNA v2.6](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6.md) - [Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/introduction-to-dragen-tso-500-ctdna-analysis-software-v2.6.md) - [Getting Started](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started.md) - [Installation of TSO 500 ctDNA v2.6.0, v2.6.1 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started/installation-of-tso-500-ctdna-v2.6.0-v2.6.1-on-standalone-dragen-server.md) - [Installation of TSO 500 ctDNA v2.6.2, v2.6.3, v2.6.4 on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started/installation-of-tso-500-ctdna-v2.6.2-v2.6.3-v2.6.4-on-standalone-dragen-server.md) - [Getting Started on Illumina Connected Analytics](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started/getting-started-on-illumina-connected-analytics.md) - [Installation of NovaSeq 6000Dx TSO 500 ctDNA Analysis Application](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started/installation-of-novaseq-6000dx-tso-500-ctdna-analysis-application.md): Instructions to install DRAGEN TSO 500 ctDNA Analysis Application on NovaSeq 6000Dx (RUO mode) - [Run Planning](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning.md) - [Sample Sheet Introduction](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/sample-sheet-introduction.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/sample-sheet-requirements.md): DRAGEN TSO 500 ctDNA Analysis Software has optional and required fields that are required in addition to general sample sheet requirements. Follow the steps below to create a valid samplesheet. - [Sample Sheet Creation in BaseSpace Run Planning tool](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/sample-sheet-creation-in-basespace-run-planning-tool.md) - [Multi-Assay Flow Cells](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/multi-assay-flow-cells.md): How to plan a run and analyze data with multiple assays loaded individually per lane on one flow cell. - [NovaSeq 6000Dx Run Set Up](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/novaseq-6000dx-run-set-up.md): The following instructions describe steps to set up a run on NovaSeq 6000Dx Analysis Application. - [Sample Sheet Templates](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/sample-sheet-templates.md): Sample Sheet templates for TSO 500 ctDNA standalone DRAGEN server and ICA manual launch analysis can be found in the table below. For auto-launch compatible sample sheets, use BaseSpace Run Planner. - [Launching Analysis](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis.md) - [Analysis Launch on Standalone DRAGEN Server](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-standalone-dragen-server.md) - [Command-Line Options](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-standalone-dragen-server/command-line-options.md) - [Analysis Launch on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-ica.md) - [Auto-Launch of DRAGEN TSO 500 ctDNA Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-ica/auto-launch-of-dragen-tso-500-ctdna-analysis-on-ica.md) - [Auto-Launch with FASTQs generated by Standalone BCL Convert Pipeline (Start from FASTQ)](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-ica/auto-launch-of-dragen-tso-500-ctdna-analysis-on-ica/auto-launch-with-fastqs-generated-by-standalone-bcl-convert-pipeline-start-from-fastq.md) - [Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/analysis-launch-on-ica/manual-launch-of-dragen-tso-500-ctdna-analysis-on-ica.md) - [Input Checks](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis/input-checks.md): Items to check before submitting your analysis - [Analysis Output](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output.md) - [Combined Variant Output](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/combined-variant-output.md) - [Metrics Output](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/metrics-output.md) - [Coverage Reports](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/coverage-reports.md) - [Block List](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/block-list.md) - [Analysis Methods](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods.md) - [FastQ Generation](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fastq-generation.md) - [Mapping and Alignment](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/mapping-and-alignment.md) - [Small Variants](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/small-variants.md) - [Fusions](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fusions.md) - [CNV](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/cnv.md) - [TMB](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/tmb.md) - [MSI](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/msi.md) - [Maximum Somatic VAF](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/max-somatic-vaf.md) - [Quality Control](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control.md) - [Run QC](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control/run-qc.md) - [Sample QC](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control/sample-qc.md) - [Contamination](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control/contamination.md) - [DNA Expanded Metrics](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control/dna-expanded-metrics.md) - [Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/troubleshooting.md) - [Revision History](https://help.connected.illumina.com/tso500/reference/resources-references.md) ## Emedgene - [Get started with Emedgene](https://help.connected.illumina.com/emedgene/get-started-with-emedgene/readme.md) - [How can Emedgene help you solve a case?](https://help.connected.illumina.com/emedgene/get-started-with-emedgene/how_can_emedgene_help_you_solve_a_case.md) - [Getting around the platform](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform.md) - [Top navigation panel](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/top_navigation_panel.md) - [Emedgene applications menu](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/emedgene_applications_menu.md) - [Dashboard tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/dashboard.md) - [Cases tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab.md) - [Cases table](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/cases_table.md) - [Cases table navigation panel](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/cases-table-navigation-panel.md) - [Case details](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details.md) - [Case info](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/case-info.md) - [Family tree](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/family-tree.md) - [Activity](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/activity.md) - [How to open a case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-open-a-case.md) - [How to customize Cases table view](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-customize-cases-table-view.md) - [How to label a case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/labeling_a_case.md) - [How to filter cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-filter-cases.md) - [How to search for cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/browse_and_select_cases.md) - [How to group cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-group-cases.md) - [How to sort cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-sort-cases.md) - [How to delete cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-delete-cases.md) - [Help](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/help.md) - [Okta identity management](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/okta_identity_management.md) - [Managing data storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage.md) - [Manage data storages](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/manage_data_storages.md) - [Manage S3 credentials](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/manage_s3_credentials.md) - [Manage ICA storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/manage-ica-storage.md) - [Storage providers](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/storage-providers.md) - [Manage Azure Blob storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/storage-providers/manage_azure_blob_data_storage.md) - [Manage Google Cloud storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/storage-providers/manage-gcs-storage-v37.0+.md) - [Manage BaseSpace storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/storage-providers/manage-basespace-storage.md) - [Bring Your Own Bucket](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/bring-your-own-bucket.md) - [Bring Your Own Key](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/managing_data_storage/bring-your-own-key.md) - [Launching analysis](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis.md) - [Creating a single case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case.md) - [1. Select sample type](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/select_sample_type.md) - [2. Family tree](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree.md) - [Creating a family tree](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/create_a_family_tree.md) - [Family tree legend](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/family_tree_legend.md) - [Adding a sample](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/add_a_sample.md) - [Adding patient info for the proband](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/adding_patient_info_for_the_proband.md) - [Adding patient info for the non-proband samples](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/adding_patient_info_for_the_non-proband_samples.md) - [Secondary findings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/secondary_findings.md) - [Supported parental ethnicities](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/2.-family-tree/supported_parental_ethnicities.md) - [3. Case info](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info.md) - [Case type and region of interest](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info/case-type-and-region-of-interest.md) - [Default region of interest kits](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info/case-type-and-region-of-interest/genomic_regions_by_case_type.md) - [Sequencing information](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info/sequencing-information.md) - [Select a gene list](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info/gene_list.md) - [Select a preset group](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/3.-case-info/preset_groups.md) - [Creating multiple cases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_multiple_cases.md) - [Batch case upload from platform](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/batch_case_upload.md) - [CSV format requirements for case upload](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/csv_format_requirements.md) - [Batch case upload via CLI](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/batch-case-upload-via-cli.md) - [Supported variant callers](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/supported-vcfs-variant-callers.md) - [Formatting DRAGEN STR VCF files for Emedgene](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/supported-vcfs-variant-callers/how_do_i_prepare_vcf_files_generated_by_dragen_str_to_be_used_as_input_for_emedgene.md) - [Tertiary analysis pipeline](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline.md) - [Supported reference genome assemblies](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/which_reference_genomes_can_i_use.md) - [Transcript prioritization logic](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_analyze_prioritize_transcripts.md) - [Emedgene annotations and update frequency](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotation_updates.md) - [Variant effect and severity calculation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_calculate_variant_effect_and_severity.md) - [Integrating variant annotations from multiple sources](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how-does-emedgene-analyze-merge-variants-from-different-sources.md) - [Processing multi-nucleotide variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how_are_mnvs_handled_on_the_platform.md) - [Annotations from organization databases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md) - [Joint calling in Emedgene](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_joint_calling_work_on_emedgene.md) - [Tertiary analysis of STR variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/str_calling_and_interpretation.md) - [Reviewing a case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case.md) - [Individual case page](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/individual_case_page.md) - [Case status](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status.md) - [Case statuses in a case lifecycle](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status/out-of-the-box-case-statuses.md) - [Case progress indicator (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status/case-progress-indicator-v100.40.0+.md) - [How to update a case status](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status/how-to-update-a-case-status.md) - [Individual case page: Top bar](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/individual-case-page-top-bar.md) - [Candidates tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/candidates-tab.md) - [Reviewing the Candidates tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/candidates-tab/reviewing-the-candidates-tab.md) - [Most Likely Candidates and Candidates](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/candidates-tab/most_likely_candidates_and_candidates.md) - [Lab tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab.md) - [Summary dashboard](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/summary-dashboard.md) - [Sequencing lab information section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sequencing-lab-information-section.md) - [Case quality section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/case-quality-section.md) - [Sample quality section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section.md) - [NGS sample quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics.md) - [NGS sample quality](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sample-quality.md) - [NGS sex validation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md) - [Ploidy](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ploidy.md) - [Contamination](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/contamination.md) - [Coverage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/coverage.md) - [Percentage of mapped reads](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/percentage-of-mapped-reads.md) - [Sequencing error rate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/sequencing-error-rate.md) - [Array sample quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics.md) - [Array sample quality](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sample-quality.md) - [Array sex validation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sex-validation.md) - [Autosomal call rate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/autosomal-call-rate.md) - [Call rate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/call-rate.md) - [Log R deviation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/log-r-deviation.md) - [DRAGEN QC report](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md) - [Requirements by case type](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report.md) - [Prepare QC files for a NGS VCF case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report/how-to-i-prepare-metrics-files-generated-by-dragen-to-be-used-as-input-for-emedgene.md) - [Download DRAGEN QC metrics files](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/download-dragen-qc-metrics-files.md) - [Pedigree section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/pedigree-section.md) - [Genes coverage section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/genes-coverage-section.md) - [Genome view tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/genome-overview.md) - [Analysis tools tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+.md) - [Variant table](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table.md) - [Variant table columns](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/variant_table_columns.md) - [Variant table row formatting](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/variant-table-row-formatting.md) - [Variant table view customization](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/variant-table-view-customization.md) - [Multi-selection of variants and bulk actions](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/multiselection_of_variants_and_bulk_actions_-340+.md) - [View / Unview variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/multiselection_of_variants_and_bulk_actions_-340+/view-unview-variants.md) - [Assign / Clear tags](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/multiselection_of_variants_and_bulk_actions_-340+/assign-clear-tags.md) - [Assign / Clear pathogenicity](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/multiselection_of_variants_and_bulk_actions_-340+/assign-clear-pathogenicity.md) - [Export selected variants to Curate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/multiselection_of_variants_and_bulk_actions_-340+/export-selected-variants-to-curate.md) - [Manually add variants to a delivered case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/manually_add_variants_to_a_delivered_case.md) - [Download variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/download_variants.md) - [Filtering panel](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel.md) - [Variant search](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/variant_search.md) - [Filters tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters.md) - [Simple filter operators mode](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode.md) - [Quality filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/quality_filters.md) - [Polymorphism filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/polymorphism_filters.md) - [Variant type filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/variant_type_filters.md) - [Variant effect filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/variant_effect_filters.md) - [In silico predictions filters (v37.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/in-silico-predictions-filters.md) - [Gene filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/gene_filters.md) - [Phenomatch filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/phenomatch_filters.md) - [Inheritance filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/inheritance_filters.md) - [Zygosity filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/zygosity_filters.md) - [Evidence & Tags filters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/user_filters.md) - [Advanced filter operators mode (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/advanced-filter-operators-mode-v100.40.0+.md) - [How filtering works in the Advanced filter operators mode](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/advanced-filter-operators-mode-v100.40.0+/how-filtering-works-in-the-advanced-filter-operators-mode.md) - [Build an advanced filtering query](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/advanced-filter-operators-mode-v100.40.0+/build-an-advanced-filtering-query.md) - [Filter list for Advanced filter operators mode](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/advanced-filter-operators-mode-v100.40.0+/v100.40.0+-filter-list.md) - [Presets tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/presets.md) - [Creating a preset](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/presets/creating-a-preset.md) - [Using presets in case review](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/presets/using-presets-in-case-review.md) - [Creating a custom preset group](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/presets/creating-a-custom-preset-group.md) - [Custom tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/custom-tab.md) - [Using presets from a custom preset group in case review](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/custom-tab/using-presets-from-a-custom-preset-group-in-case-review.md) - [Viewing modes (v100.39.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/viewing-modes.md) - [Versions tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/versions_tab.md) - [Evidence page](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/evidence_page.md) - [Phenotypic match](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/phenotypic-match.md) - [Phenotypic match models](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotypic-match-models.md) - [Phenotypic match strength](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotypic_match_strength.md) - [Phenotype weights (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotype-weights-v100.40.0+.md) - [Editing a delivered case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/editing_an_existing_case.md) - [Reflex genetic testing](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/reflex_genetic_testing.md) - [Variant zygosity notations](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/variant_zygosity_notations.md) - [Reviewing a variant](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page.md) - [Variant page](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page.md) - [Variant page top bar](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page_top_bar.md) - [Variant tagging widget](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_tagging_widget.md) - [Multiple tags](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_tagging_widget/multiple-tags.md) - [Curate actions in Analyze](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/curate-actions-in-analyze.md) - [Export to Curate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/curate-actions-in-analyze/export-to-curate.md) - [Update in Curate (v38.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/curate-actions-in-analyze/update-in-curate-v38.0+.md) - [Open in Curate](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/curate-actions-in-analyze/open-in-curate.md) - [Summary tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/summary_section.md) - [Clinical significance tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section.md) - [Variant info](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info.md) - [Transcript](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/transcript.md) - [Resources](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/resources.md) - [In silico predictions](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/in-silico-predictions.md) - [Gene metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-metrics.md) - [Clinical significance](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/clinical-significance.md) - [Gene-related diseases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-related-diseases.md) - [Quality tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section.md) - [Variant quality summary](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/variant-quality-summary.md): Understand the overall quality signal shown for a variant across samples. - [Quality metrics per variant type](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type.md) - [SNV, MNV, and indel quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/snv-mnv-and-indel-quality-metrics.md) - [CNV quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/cnv-quality-metrics.md) - [SV quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/sv-quality-metrics.md) - [STR quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/str-quality-metrics.md) - [Haplotype variant quality metrics](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/haplotype-variant-quality-metrics.md) - [Allele distribution](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/allele-distribution.md): Review how sequencing reads support reference and alternate alleles. - [Visualization tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) - [Population statistics tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/population_statistics_section.md) - [Connected variants tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/connected-variants-tab.md) - [Related cases tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section.md) - [Network data view controls](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/network-data-view-controls.md) - [Pathogenicity trend bar](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/pathogenicity-trend-bar.md) - [Related cases table](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/related-cases-table.md) - [CNV overlap percentage filter](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/cnv_overlap_percentage.md) - [One-way CNV annotation overlap](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/cnv_overlap_percentage/one-way-cnv-annotation-overlap.md) - [Evidence tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section.md) - [ACMG SNV Classification wizard](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section/acmg_snv_classification_wizard.md) - [Logic behind ACMG classification of SNVs](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section/logic_behind_acmg_classification_of_snvs.md) - [ACMG SNV criteria evaluation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section/acmg-snv-criteria-evaluation.md) - [ACMG CNV Classification wizard](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section/acmg_cnv_classification_wizard.md) - [Variant page sidebar](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page_sidebar_-229+.md) - [Case completion and reporting](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting.md) - [Completing case interpretation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting/completing-case-interpretation.md) - [Finalizing a case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting/finalizing_a_case.md) - [Reporting](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting/clinical_report.md) - [Variant visualization](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization.md) - [Variant visualization tool](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool.md) - [Track Manager (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager-v100.40.0+.md) - [Track Manager (v100.39.0 and older)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/viewing-modes.md) - [Visualization tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) - [Default tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/default-tracks.md) - [Curated data tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/curated-data-tracks.md) - [Knowledge base tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/knowledge-base-tracks.md) - [Population data tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/population-data-tracks.md) - [Additional tracks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/additional-tracks.md): Optional alignment, signal, and structural tracks in the variant visualization tool. - [Visual aids](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visual-aids.md) - [Open the visualization tool in a popup window (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/open-the-visualization-tool-in-a-popup-window-v100.40.0+.md) - [Manually add variant from IGV](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/manually-add-variant-from-igv.md) - [Variant visualization setup](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant_visualization_setup.md) - [Enabling visualization for a VCF case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/enabling_visualization_for_a_vcf_case.md) - [Integration between Emedgene and desktop IGV](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/integration_between_emedgene_and_desktop_igv.md) - [Loading alignment files to your desktop IGV](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/loading_alignment_files_to_your_desktop_igv_-320+.md) - [Analyze Network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network.md) - [Analyze Network Setup](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/analyze_network_setup.md) - [Network sharing configuration](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/network_sharing_configuration.md) - [Case subject consent for extended sharing](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/case_subject_consent_for_extended_sharing.md) - [Public vs Private network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/public_vs_private_network.md) - [Create a network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/create_a_network.md) - [Set network data sharing policy](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/set_network_data_sharing_policy.md) - [Leave a network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/leave_a_network.md) - [Delete a network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/analyze_network/delete_a_network.md) - [Settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings.md) - [My settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/my_settings.md) - [Management](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management.md) - [Illumina support access](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/illumina-support-access.md) - [Storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/storage.md) - [S3 credentials](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/s3-credentials.md) - [Case statuses](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/test-statuses.md) - [Test settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/test-settings.md) - [Groups](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/groups.md) - [Webhooks](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/management/webhooks.md) - [User access management](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/user_roles.md) - [User access management in Illumina environments](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/user_roles/user-access-management-in-illumina-environments.md) - [User access management in legacy Emedgene environments](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/user_roles/user-access-management-in-legacy-emedgene-environments.md) - [IAM scopes/Emedgene roles](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md) - [Network](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/network.md) - [Organization settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+.md) - [General](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/general.md): General settings and organization information - [Workbench & Pipeline](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline.md) - [AI Shortlist module](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/ai-shortlist-module.md) - [AI ACMG module (v100.39.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/ai-acmg-module-v100.39.0+.md) - [Pipeline versions](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/pipeline-versions.md) - [Organization DB management](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md) - [Organization databases](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/organization-databases.md) - [Configuring an organization database](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database.md) - [Creating a database VCF file](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file.md) - [Creating an internal database VCF file](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file/creating-an-internal-database-vcf-file.md) - [Creating an external database VCF file](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file/creating-an-external-database-vcf-file.md) - [Registering a database](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/registering-a-database.md) - [Modifying database settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md) - [SV annotation thresholds](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/sv-annotation-thresholds.md) - [Environment](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment.md) - [Organization URL (ILMN clouds)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/organization-url-ilmn-clouds.md) - [Platform version](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/platform-version.md) - [How do I check my platform version?](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/platform-version/how_do_i_check_the_version_of_my_environment.md) - [Case identifier](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/case-identifier.md) - [Default page](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/default-page.md) - [Analysis tools columns order](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/analysis-tools-columns-order.md) - [Visualization tracks order (v100.40.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/environment/visualization-tracks-order-v100.40.0+.md) - [Case settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/case-settings.md) - [Variant tags](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/case-settings/variant-tags.md) - [Lab workflow](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow.md) - [Presets](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/presets.md) - [Preset groups](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/preset-groups.md) - [Legacy preset groups](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/preset-groups/legacy-preset-groups.md) - [Default preset group](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/default-preset-group.md) - [Kit Management](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management.md) - [BED files](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files.md) - [Required format for a BED file defining a kit](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files/what_is_the_required_format_for_a_bed_file_defining_a_kit.md) - [Panel of normals (PON)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon.md) - [Attaching a PON to a Coverage BED kit](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/attaching-a-pon-to-a-coverage-bed-kit.md) - [Removing PON files from storage](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/removing-pon-files-from-storage.md) - [Creating a PON for Emedgene using BaseSpace Baseline Builder](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/creating-a-pon-for-emedgene-using-basespace-baseline-builder.md) - [Quality parameters](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+.md) - [NGS quality](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+/ngs-quality.md) - [Array sample quality](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+/array-sample-quality.md) - [Integration (v100.39.0+)](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/integration-v100.39.0+.md) - [Encryption settings](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/integration-v100.39.0+/encryption-settings.md) - [Integrations](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations.md) - [Automatic Case Creation from ICA - Cyto Array Analysis](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/automatic-case-creation-from-ica-cyto-array-analysis.md): Seamless end-to-end workflow from scanner to tertiary analysis with no human intervention. - [API Beginner Guide](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/api-beginner-guide.md) - [Advanced API Implementations](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/advanced-api-implementations.md): This page provides several code examples demonstrating how to use the platform for common scenarios. While you don't need to follow or implement every example, they can serve as useful starting points - [API Key Generation](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/api-key-generation.md) - [BSSH Integration](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/bssh-integration.md): Please contact Tech Support with the subject "BaseSpace Emedgene Connect app" for assistance. - [ICA Integration](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/ica-integration.md) - [Webhook Integration](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/integrations/webhook-integration.md) - [Troubleshooting](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/troubleshooting.md) - [Which browser should I use with Emedgene?](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/troubleshooting/which_browser_should_i_use_with_emedgene.md) - [How do I use developer tools to collect logs?](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/troubleshooting/how_do_i_use_developer_tools_to_collect_logs.md) - [Performance issues troubleshooting](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/troubleshooting/performance_issue_troubleshooting.md) - [Curate overview](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_overview.md) - [Emedgene Applications menu](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_overview/emedgene_applications_menu.md) - [Curate navigation panel](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_overview/curate_navigation_panel.md) - [Genome assemblies supported by Curate](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_overview/genome_assemblies_supported_by_curate.md) - [Curate Variants](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants.md) - [Curate Variant table](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/curate_variant_table.md) - [Curate Variant page](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/curate_variant_page.md) - [Curate Variant annotations in the case](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/curate_variant_annotations_in_the_case.md) - [Adding variants to Curate](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/adding-variants-to-curate.md) - [Adding a single variant to Curate](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/adding-variants-to-curate/adding-a-single-variant-to-curate.md) - [Adding or updating multiple variants in Curate](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/adding-variants-to-curate/adding-or-updating-multiple-variants-in-curate.md) - [CSV format requirements for variant upload](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/adding-variants-to-curate/adding-or-updating-multiple-variants-in-curate/csv-format-requirements-for-variant-upload.md) - [Exporting a variant from Analyze](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/adding-variants-to-curate/exporting-a-variant-from-analyze.md) - [Deleting a variant from Curate (v100.39.0+)](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_variants/how-to-delete-a-variant-in-curate-v100.39.0+.md) - [Curate Genes](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_genes_2_28.md) - [Curate Gene table](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_genes_2_28/curate_gene_table.md) - [Curate Gene page](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_genes_2_28/curate_gene_page.md) - [How to add a gene to Curate](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/curate_genes_2_28/how_to_add_a_gene_to_curate.md) - [Import Curate annotations to the case](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/import_curate_annotations.md) - [Import Curate Variant annotations to the case](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/import_curate_annotations/import_curate_variant_annotations_to_the_case_-300+.md) - [Import Curate Gene annotations to the case](https://help.connected.illumina.com/emedgene/emedgene-curate-manual/import_curate_annotations/import_curate_gene_annotations_to_the_case_-300+.md) - [Integrations](https://help.connected.illumina.com/emedgene/integrations.md) - [API Beginner Guide](https://help.connected.illumina.com/emedgene/integrations/api-beginner-guide.md): This guide provides instructions on using the Curate API to create, update, and search for variants and genes, and on exporting Curate data to a CSV. - [All FAQ](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq.md) - [Can I analyze Illumina Complete Long Reads in Emedgene?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/can_i_analyze_illumina_complete_long_reads_in_emedgene.md) - [How do I analyze mtDNA variants?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how_do_i_analyze_mtdna_variants.md) - [Can I use exome data for CNV detection?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/can_i_use_exome_data_for_cnv_detection.md) - [How do I move between organizations?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how_do_i_move_between_organizations.md) - ["Failed to generate report". What should I do?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/failed_to_generate_report_what_should_i_do.md) - [How are timekeeping and log timestamps kept accurate and consistent?](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how-are-timekeeping-and-log-timestamps-kept-accurate-and-consistent.md) - [Workbench & Pipeline Updates](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates.md): Release summary table with convenient links to release notes. - [New in Emedgene V100.40.0 (March 30th, 2026)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.40.0-march-30th-2026.md) - [V100.40 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.40.0-march-30th-2026/v100.40-patches.md) - [New in Emedgene V100.39.0 (October 16th, 2025)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.39.0-october-16th-2025.md) - [V100.39 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.39.0-october-16th-2025/v100.39-patches.md) - [New in Emedgene V38.0 (June 3rd, 2025)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v38-june-3rd-2025.md) - [V38 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v38-june-3rd-2025/v38-patches.md) - [New in Emedgene V37.0 (February 20, 2025)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new_in_emedgene_37_-february_17_2025.md) - [V37 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new_in_emedgene_37_-february_17_2025/v37-patches.md) - [New in Emedgene V36.0 (October 8 2024)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new_in_emedgene_36_-october_8th_2024.md) - [V36 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/new_in_emedgene_36_-october_8th_2024/v36-patches.md) - [More release notes](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes.md) - [New in Emedgene V35.0 (May 22nd 2024)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_35_-may_22nd_2024.md): AI in the analysis tools, multiple panel workflows, haplotypes - [V35 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_35_-may_22nd_2024/v35-patches.md) - [New in Emedgene V34.0 (January 28th 2024)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_34_-january_28th_2024.md) - [V34 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_34_-january_28th_2024/v34-patches.md) - [New in Emedgene V33.0 (September 6th 2023)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_33_-september_6th_2023.md) - [V33 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_33_-september_6th_2023/v33-patches.md) - [New in Emedgene V32.0 (June 8th 2023)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_32_-june_8th_2023.md) - [New pipeline 32 (June 8th 2023)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_32_-june_8th_2023/new_pipeline_32_-june_8th_2023.md) - [V32 Patches](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_32_-june_8th_2023/v32-patches.md) - [New in emedgene 31 (March 1st 2023)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_31_-march_1st_2023.md) - [New in Emedgene 30 (January 8th 2023)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_30_-january_8th_2023.md) - [New in Emedgene 2.29 (August 25 2022)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_229_-august_25_2022.md) - [New pipeline 5.29 (May 1st 2022)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_pipeline_529_-may_1st_2022.md) - [New in Emedgene 2.28 (May 1 2022)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_228_-may_1_2022.md) - [New in Emedgene 2.27 (March 7, 2022)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_227_-march_7-_2022.md) - [New in Emedgene 2.26 (Dec 14, 2021)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_226_-dec_14-_2021.md) - [New in Emedgene 2.24-2.25 (Aug 11, 2021)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_224-225_-aug_11-_2021.md) - [New in Emedgene 2.23 (Jun 15, 2021)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_223_-jun_15-_2021.md) - [New in Emedgene 2.19-2.22 (Apr 8, 2021)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_219-222_-apr_8-_2021.md) - [New in Emedgene 2.16-2.19 (Dec 7, 2020)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_216-219_-dec_7-_2020.md) - [New in Emedgene 2.12-2.16 (Oct 18, 2020)](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_212-216_-oct_18-_2020.md) - [Change log](https://help.connected.illumina.com/emedgene/release-notes/change_log.md) - [Change log pipeline v34](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_pipeline_v34.md) - [Change log pipeline 31](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_pipeline_31.md) - [Change log workbench 31](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_workbench_31.md) - [Change log pipeline 30](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_pipeline_30.md) - [Change log workbench 30](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_workbench_30.md) - [Change log workbench 2.29](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_workbench_229.md) - [Change log pipeline 5.29](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_pipeline_529.md) - [Change log workbench 2.28](https://help.connected.illumina.com/emedgene/release-notes/change_log/change_log_workbench_228.md) - [Privacy, Security & Compliance](https://help.connected.illumina.com/emedgene/legal/privacy-security-and-compliance.md) - [Release Policy](https://help.connected.illumina.com/emedgene/legal/release_policy.md) ## Illumina Connected Insights - [Welcome](https://help.connected.illumina.com/connected-insights/overview/readme.md) - [Typical user actions](https://help.connected.illumina.com/connected-insights/overview/readme/o-typicaluseractions.md) - [What's New](https://help.connected.illumina.com/connected-insights/overview/whats-new.md) - [Release Notes](https://help.connected.illumina.com/connected-insights/overview/whats-new/rar-release-notes.md) - [How to Upgrade (Cloud)](https://help.connected.illumina.com/connected-insights/overview/whats-new/software-update-connected-insights-cloud.md) - [Local Software Update](https://help.connected.illumina.com/connected-insights/overview/whats-new/software-update.md) - [Webinars](https://help.connected.illumina.com/connected-insights/overview/webinars.md) - [Configuration](https://help.connected.illumina.com/connected-insights/configure/configuration.md) - [Custom Case Data](https://help.connected.illumina.com/connected-insights/configure/configuration/c-custom-case-data-definition.md) - [Pipeline and QC Configuration](https://help.connected.illumina.com/connected-insights/configure/configuration/c-pipeline-and-qc-configuration.md) - [Preferred Transcripts](https://help.connected.illumina.com/connected-insights/configure/configuration/c-preferred-transcripts.md) - [Custom Annotations](https://help.connected.illumina.com/connected-insights/configure/configuration/c-custom-annotations.md) - [Disease Configuration](https://help.connected.illumina.com/connected-insights/configure/configuration/c-disease-configuration.md) - [Variant Filters](https://help.connected.illumina.com/connected-insights/configure/configuration/c-variant-filters.md) - [Variant Flag Groups](https://help.connected.illumina.com/connected-insights/configure/configuration/c-variant-flag-groups.md) - [Actionability Classifications](https://help.connected.illumina.com/connected-insights/configure/configuration/c-custom-actionability-classification.md) - [Report Templates](https://help.connected.illumina.com/connected-insights/configure/configuration/reports-report-templates.md) - [Customizations](https://help.connected.illumina.com/connected-insights/configure/configuration/reports-report-templates/reports-report-customizations.md) - [Report Automation](https://help.connected.illumina.com/connected-insights/configure/configuration/c-automation.md) - [Lab Information](https://help.connected.illumina.com/connected-insights/configure/configuration/c-lab-information.md) - [Test Definitions](https://help.connected.illumina.com/connected-insights/configure/configuration/c-test-definition-setup.md) - [Data Upload](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction.md) - [Data Upload from User Storage (Connected Insights - Cloud and Connected Insights - Local)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-user-storage.md) - [Data Upload from ICA or BSSH (Connected Insights - Cloud)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-ica.md) - [Supported Pipelines](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.6.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.2.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.6.1 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.1-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.6.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.1.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.6.0 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.0-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.6.0](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.0.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.5.3 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.5.3-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.5.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.5.3.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.5.2 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.5.2-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.5.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.5.2.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.1.2 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.1.2-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.1.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.1.2.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.1.1 (with HRD)](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.1.1-with-hrd.md) - [DRAGEN TruSight Oncology 500 Analysis Software v2.1.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.1.1.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.6.4.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.6.3.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.6.2.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.6.1.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.0](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.6.0.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.5.0](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.5.0.md) - [DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.1.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-ctdna-analysis-software-v2.1.1.md) - [DRAGEN Solid WGS Tumor Normal v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-solid-wgs-tn-v4.4.md) - [DRAGEN Heme v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-heme-v4.4.md) - [DRAGEN Heme v1.0](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-heme-v1.0.md) - [DRAGEN Amplicon v4.5](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-amplicon-v4.5.md) - [DRAGEN Amplicon v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-amplicon-v4.4.md) - [DRAGEN Amplicon v4.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-amplicon-v4.3.md) - [DRAGEN Amplicon v4.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-amplicon-v4.2.md) - [DRAGEN Amplicon v4.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-amplicon-v4.1.md) - [DRAGEN RNA v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-rna-v4.4.md) - [DRAGEN RNA v4.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-rna-v4.3.md) - [DRAGEN RNA v4.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-rna-v4.2.md) - [DRAGEN RNA v4.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-rna-v4.1.md) - [DRAGEN Somatic Enrichment and Whole Genome v4.5](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-enrichment-and-whole-genome-v4.5.md) - [DRAGEN Somatic Enrichment and Whole Genome v4.4.6](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-enrichment-and-whole-genome-v4.4.6.md) - [DRAGEN Somatic Enrichment v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-enrichment-v4.4.md) - [DRAGEN Somatic Enrichment v4.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-enrichment-v4.3.md) - [DRAGEN Somatic Enrichment v4.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-enrichment-v4.2.md) - [DRAGEN Somatic Enrichment v4.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-enrichment-v4.1.md) - [DRAGEN for Illumina cfDNA Prep with Enrichment v4.0.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-for-illumina-cfdna-prep-with-enrichment-v4.0.3.md) - [DRAGEN Somatic Whole Genome v4.5](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-whole-genome-v4.5.md) - [DRAGEN Somatic Whole Genome v4.4](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-whole-genome-v4.4.md) - [DRAGEN Somatic Whole Genome v4.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-whole-genome-v4.3.md) - [DRAGEN Somatic Whole Genome v4.2](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-whole-genome-v4.2.md) - [DRAGEN Somatic Whole Genome v4.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-somatic-whole-genome-v4.1.md) - [TruSight Tumor 170 Local App v2.0.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/trusight-tumor-170-local-app-v2.0.1.md) - [Local Run Manager TruSight Tumor 15 Analysis Module v2.1](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/local-run-manager-trusight-tumor-15-analysis-module-v2.1.md) - [Archer VariantPlex Pipeline v7.3](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/archer-variantplex-pipeline-v7.3.md) - [Pillar Biosciences RUO PiVAT Pipeline v2024](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/pillar-biosciences-ruo-pivat-pipeline-v2024.md) - [Custom Pipeline Configuration](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration.md) - [VCF Input Requirement](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/du-vcf-input-requirement.md) - [TMB, MSI, GIS Input Requirement](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement.md) - [TMB JSON Minimal](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/tmb-json-min.md) - [TMB JSON Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/tmb-json-full.md) - [TMB CSV Minimal](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/tmb-csv-min.md) - [TMB CSV Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/tmb-csv-full.md) - [MSI JSON Minimal](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/msi-json-min.md) - [MSI JSON Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/msi-json-full.md) - [GIS JSON Minimal](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/gis-json-min.md) - [GIS JSON Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/gis-json-full.md) - [HRD CSV Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/hrd-csv-full.md) - [HLA TSV Full](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-pipeline-configuration/tmb-msi-gis-input-requirement/hla-tsv-full.md) - [Custom Case Data Upload](https://help.connected.illumina.com/connected-insights/configure/configuration/du-introduction/du-custom-case-dataupload.md) - [Upload Assertions](https://help.connected.illumina.com/connected-insights/configure/du-assertion-upload.md) - [Local Installation Guide](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide.md) - [Overview](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-introduction.md) - [Prerequisites](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-prerequisites.md) - [Download Connected Insights Package](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-downloaderutility.md) - [Install Illumina Administration Console Software](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-installconnectedinsightssoftware.md) - [Sign In to Illumina Connected Insights software](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-signintoconnectedinsights.md) - [Install Connected Insights - Local Software](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-installconnectedinsightssoftware-1.md) - [Install License Files](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-installlicensefile.md) - [Installation Status Messages](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/ici-installationstatusmsg.md) - [Local Configurations](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/admin-overview.md) - [Administration Console (Connected Insights - Local)](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/admin-overview/admin-administration-console.md) - [Configure External storage](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/admin-overview/configure-storage.md) - [Data Backup (Connected Insights - Local)](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/admin-overview/troub-data-backup.md) - [How To](https://help.connected.illumina.com/connected-insights/configure/local-installation-guide/admin-overview/how-to.md) - [Cases Page](https://help.connected.illumina.com/connected-insights/manage-cases/cm-introduction.md) - [Case Metadata Upload](https://help.connected.illumina.com/connected-insights/manage-cases/cm-introduction/cm-metadata-upload.md) - [Audit Log](https://help.connected.illumina.com/connected-insights/manage-cases/al-introduction.md) - [Case Page](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-introduction.md) - [Case Details](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-cases-details.md) - [Merge Cases](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-cases-details/cm-merge-cases.md) - [Results / Overview Tab](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-overview-tab.md) - [Classification & Risk Stratification Prediction](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-overview-tab/classification-and-risk-stratification-prediction.md) - [Visualize Tab](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-visualize-tab.md) - [Variants Tab](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid.md) - [Modify Columns](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/inter-modify-variant-grid.md) - [Apply Variant Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction.md) - [Filter by Variant Category](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-filter-by-variant-category.md) - [Variant Details Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-details-filters.md) - [Variant Quality Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-quality-filters.md) - [Functional Impact Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-functional-impact-filters.md) - [Disease Association Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-disease-association-filters.md) - [Variant Frequency Filters](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-frequency-filters.md) - [Flags Filter](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-flags-filter.md) - [Filtering Logic](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-filtering-logic.md) - [IGV Visualizations](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-variant-grid/inter-igv-visualizations.md) - [Lab QC Tab](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-lab-qc-tab.md) - [Report Tab](https://help.connected.illumina.com/connected-insights/interpret-and-report/cm-report-tab.md) - [View Biomarker Details](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction.md) - [Biological Classification](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-biological-classification-assertions.md) - [Actionability](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-actionability.md) - [Clinical Trials](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-clinical-trials.md) - [Oncogenicity Prediction](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-oncogenicity-prediction.md) - [Visualize](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-visualize.md) - [Variant Overview](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-variant-overview.md) - [Gene Overview](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-gene-overview.md) - [Cancer Datasets](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-cancer-data-sets.md) - [Computer Predictors](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-computer-predictors.md) - [Population](https://help.connected.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-population.md) - [Interpret a Biomarker](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-interp-a-variant.md) - [Create Clinical Trials](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-interp-a-variant/inter-clinical-trial.md) - [Create Gene Descriptions](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-interp-a-variant/inter-gene-description.md) - [Manage Assertions](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-interp-a-variant/inter-manage-assertions.md) - [Variant Transcripts](https://help.connected.illumina.com/connected-insights/interpret-and-report/inter-transcripts.md) - [Add Variant](https://help.connected.illumina.com/connected-insights/interpret-and-report/add-variant.md) - [APIs](https://help.connected.illumina.com/connected-insights/resources-and-references/a-introduction.md) - [Ingest Cloud Analysis Data API (Connected Insights - Cloud Only)](https://help.connected.illumina.com/connected-insights/resources-and-references/a-introduction/a-ingest-cloud-analysis-data.md) - [Case APIs](https://help.connected.illumina.com/connected-insights/resources-and-references/a-introduction/a-case-apis.md) - [Report APIs](https://help.connected.illumina.com/connected-insights/resources-and-references/a-introduction/a-report.md) - [Audit Log APIs](https://help.connected.illumina.com/connected-insights/resources-and-references/a-introduction/a-audit-logs-api.md) - [Glossary](https://help.connected.illumina.com/connected-insights/resources-and-references/rar-acronyms-and-terms.md) - [User Roles](https://help.connected.illumina.com/connected-insights/resources-and-references/user-roles.md) - [Troubleshooting](https://help.connected.illumina.com/connected-insights/resources-and-references/troub-overview.md) - [Overview](https://help.connected.illumina.com/connected-insights/resources-and-references/troub-overview/rar-introduction.md) - [Software Errors and Corrective Actions](https://help.connected.illumina.com/connected-insights/resources-and-references/troub-overview/troub-error-currectiveaction.md) - [Technical Assistance](https://help.connected.illumina.com/connected-insights/resources-and-references/troub-overview/overview.md) - [Terms](https://help.connected.illumina.com/connected-insights/resources-and-references/terms.md) - [Security & Compliance](https://help.connected.illumina.com/connected-insights/resources-and-references/security-and-compliance.md) - [Pricing and Usage](https://help.connected.illumina.com/connected-insights/resources-and-references/usg-introduction.md) - [Release Policy](https://help.connected.illumina.com/connected-insights/resources-and-references/release-policy.md) - [Release Notes](https://help.connected.illumina.com/connected-insights/resources-and-references/rar-release-notes.md) - [5.4 Release Notes](https://help.connected.illumina.com/connected-insights/resources-and-references/rar-release-notes/5.4-release-notes.md) - [<5.4 Release Notes](https://help.connected.illumina.com/connected-insights/resources-and-references/rar-release-notes/rar-release-notes.md) ## Correlation Engine - [Release Notes](https://help.connected.illumina.com/correlation-engine/readme.md) - [Correlation Engine FAQ](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq.md) - [Single-cell analysis in Correlation Engine](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/single-cell-analysis-in-correlation-engine.md) - [Cufflinks Assembly & DE output conversion to bioset](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/cufflinks-assembly-and-de-output-conversion-to-bioset.md) - [RNA-Express output conversion to bioset](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/rna-express-output-conversion-to-bioset.md) - [RNA-Seq alignment conversion to Correlation Engine Biosets](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/rna-seq-alignment-conversion-to-correlation-engine-biosets.md) - [BaseSpace ChIP-Seq output conversion to bioset](https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/basespace-chip-seq-output-conversion-to-bioset.md) ## DRAGEN 5-base - [Introduction](https://help.connected.illumina.com/dragen-5-base/get-started/readme.md) - [BSSH Analysis Setup](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/bssh-analysis-setup.md) - [DRAGEN Germline](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/bssh-analysis-setup/dragen-germline.md) - [DRAGEN Somatic](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/bssh-analysis-setup/dragen-somatic.md) - [DRAGEN Enrichment](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/bssh-analysis-setup/dragen-enrichment.md) - [ICA Analysis Setup](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup.md) - [DRAGEN Germline Whole Genome](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-germline-whole-genome.md) - [DRAGEN Somatic](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-somatic-whole-genome.md): DRAGEN Somatic for Enrichment and Whole Genome - [DRAGEN Somatic (Whole Genome)](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-somatic-whole-genome/dragen-somatic-whole-genome.md) - [DRAGEN Somatic (Enrichment)](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-somatic-whole-genome/dragen-somatic-enrichment.md) - [DRAGEN Germline Enrichment](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-germline-enrichment.md) - [Local DRAGEN Server Analysis Setup](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/local-dragen-server-analysis-setup.md) - [Optional Setting: Min Q-Score for Methylation Calling](https://help.connected.illumina.com/dragen-5-base/run-analysis-setup/optional-setting-min-q-score-for-methylation-calling.md) - [Connected Multiomics Walkthrough](https://help.connected.illumina.com/dragen-5-base/tertiary-analysis/connected-multiomics-walkthrough.md) - [FAQs](https://help.connected.illumina.com/dragen-5-base/additional-information/faqs.md) - [Known Limitations](https://help.connected.illumina.com/dragen-5-base/additional-information/known-limitations.md) - [Key Output Files and Metrics](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics.md) - [DRAGEN Germline with CNV Variant Calling](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-cnv-variant-calling.md) - [DRAGEN Germline with Small Variant Calling](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-small-variant-calling.md) - [DRAGEN Germline with No Variant Calling](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-no-variant-calling.md) - [DRAGEN Somatic Tumor Only](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-somatic-tumor-only.md) - [DRAGEN Somatic Tumor-Normal](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-somatic-tumor-normal.md) - [DRAGEN Enrichment](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-enrichment.md) - [Pre-Sequencing and Sequencing](https://help.connected.illumina.com/dragen-5-base/additional-information/pre-sequencing-and-sequencing.md) - [NovaSeq X Run Planning - BCL Convert](https://help.connected.illumina.com/dragen-5-base/additional-information/pre-sequencing-and-sequencing/page-2.md): This page gives an overview of how to plan a sequencing run on BaseSpace for the NovaSeq X Series. - [NovaSeq 6000 Run Planning - BCL Convert](https://help.connected.illumina.com/dragen-5-base/additional-information/pre-sequencing-and-sequencing/novaseq-6000-run-planning.md): This page gives an overview of how to plan a sequencing run on BaseSpace for the NovaSeq 6000. - [NextSeq 1000/2000 Run Planning - BCL Convert](https://help.connected.illumina.com/dragen-5-base/additional-information/pre-sequencing-and-sequencing/nextseq-1000-2000-run-planning-bcl-convert.md): This page gives an overview of how to plan a sequencing run on BaseSpace for the NextSeq 1000/2000. - [Instrument Domain Set Up](https://help.connected.illumina.com/dragen-5-base/additional-information/instrument-domain-set-up.md) - [Additional Resources](https://help.connected.illumina.com/dragen-5-base/additional-information/additional-resources.md) - [Release History](https://help.connected.illumina.com/dragen-5-base/additional-information/release-history.md) ## DRAGEN miRNA - [Introduction](https://help.connected.illumina.com/dragen-mirna/readme.md) - [Counting Algorithm](https://help.connected.illumina.com/dragen-mirna/readme/counting-algorithm.md) - [Reference Database](https://help.connected.illumina.com/dragen-mirna/readme/reference-database.md) - [Read Structure](https://help.connected.illumina.com/dragen-mirna/readme/read-structure.md) - [Prerequisites](https://help.connected.illumina.com/dragen-mirna/get-started/gs-abouttheplatform.md) - [Sample Sheet Creation](https://help.connected.illumina.com/dragen-mirna/run-set-up/page.md) - [Analysis in BSSH](https://help.connected.illumina.com/dragen-mirna/running-secondary-analysis/analysis-in-bssh.md) - [Analysis in ICA](https://help.connected.illumina.com/dragen-mirna/running-secondary-analysis/analysis-in-ica.md) - [Accessing Results](https://help.connected.illumina.com/dragen-mirna/analysis-results/accessing-results.md) - [Secondary Analysis Results](https://help.connected.illumina.com/dragen-mirna/analysis-results/secondary-analysis-results.md) - [DRAGEN Report](https://help.connected.illumina.com/dragen-mirna/analysis-results/dragen-report.md) - [Demo Data](https://help.connected.illumina.com/dragen-mirna/tertiary-analysis/demo-data.md) - [Illumina Connected Multiomics](https://help.connected.illumina.com/dragen-mirna/tertiary-analysis/illumina-connected-multiomics.md): Illumina Connected Multiomics (ICM) is available for tertiary analysis of miRNA and other multiomic data. - [Common Questions](https://help.connected.illumina.com/dragen-mirna/faq/common-questions.md) - [Known Issues and Limitations](https://help.connected.illumina.com/dragen-mirna/faq/known-issues-and-limitations.md) ## DRAGEN Protein Quantification - [Introduction](https://help.connected.illumina.com/dragen-protein-quantification/get-started/readme.md) - [Prerequisites](https://help.connected.illumina.com/dragen-protein-quantification/get-started/prerequisites.md) - [Illumina Protein Prep Automation System Output Files](https://help.connected.illumina.com/dragen-protein-quantification/get-started/prerequisites/illumina-protein-prep-automation-system-output-files.md) - [Local Software Install](https://help.connected.illumina.com/dragen-protein-quantification/get-started/prerequisites/local-software-install.md) - [Run Planning with the BSSH Run Planner Tool](https://help.connected.illumina.com/dragen-protein-quantification/run-setup/page.md) - [Sample Sheet Fields](https://help.connected.illumina.com/dragen-protein-quantification/run-setup/sample-sheet-fields.md) - [Local Sample Sheet Generation Tool](https://help.connected.illumina.com/dragen-protein-quantification/run-setup/sample-sheet-generation-tool.md) - [Lane Splitting and Multi-Analysis by Project](https://help.connected.illumina.com/dragen-protein-quantification/run-setup/lane-splitting-and-project-splitting.md) - [Cloud Autolaunch Secondary Analysis](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/cloud-autolaunch-secondary-analysis.md) - [Accessing Cloud Results](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/cloud-autolaunch-secondary-analysis/accessing-cloud-results.md) - [Local Secondary Analysis](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/local-secondary-analysis.md) - [Counting and Normalization](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/counting-and-normalization.md) - [QC Summary](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/qc-summary.md) - [Interpretation of Results](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/interpretation-of-results.md) - [Common Failure Modes](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/interpretation-of-results/common-failure-modes.md) - [Metrics Appendix](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/metrics-appendix.md) - [Output Structure](https://help.connected.illumina.com/dragen-protein-quantification/output-files/output-structure.md) - [DRAGEN Report](https://help.connected.illumina.com/dragen-protein-quantification/output-files/dragen-report.md) - [ADAT Content - 9.5k](https://help.connected.illumina.com/dragen-protein-quantification/output-files/adat-content-9.5k.md) - [ADAT Content - 6k](https://help.connected.illumina.com/dragen-protein-quantification/output-files/adat-content-9.5k/adat-content-6k.md) - [Using the ADAT](https://help.connected.illumina.com/dragen-protein-quantification/after-counting-and-normalization/using-the-adat.md) - [Compatibility with Excel](https://help.connected.illumina.com/dragen-protein-quantification/after-counting-and-normalization/using-the-adat/compatibility-with-excel.md) - [Illumina Connected Multiomics Walkthrough](https://help.connected.illumina.com/dragen-protein-quantification/after-counting-and-normalization/illumina-connected-multiomics-walkthrough.md) - [FAQs](https://help.connected.illumina.com/dragen-protein-quantification/references/faqs.md) - [Known Limitations](https://help.connected.illumina.com/dragen-protein-quantification/references/known-limitations.md) - [Demo Data](https://help.connected.illumina.com/dragen-protein-quantification/references/demo-data.md) - [Acronym Glossary](https://help.connected.illumina.com/dragen-protein-quantification/references/acronym-glossary.md) - [Documentation Revision History](https://help.connected.illumina.com/dragen-protein-quantification/references/documentation-revision-history.md) ## DRAGEN Single Cell RNA - [Introduction](https://help.connected.illumina.com/dragen-single-cell-rna/readme.md) - [Prerequisites](https://help.connected.illumina.com/dragen-single-cell-rna/get-started/gs-prerequisites.md) - [Run Planning in BaseSpace Sequence Hub](https://help.connected.illumina.com/dragen-single-cell-rna/run-set-up-in-bssh/run-planning.md) - [Sample Sheet Requirements](https://help.connected.illumina.com/dragen-single-cell-rna/run-set-up-in-bssh/run-planning/sample-sheet-requirements.md) - [Manual Launch on BaseSpace](https://help.connected.illumina.com/dragen-single-cell-rna/run-set-up-in-bssh/manual-launch.md) - [Installation and Setup](https://help.connected.illumina.com/dragen-single-cell-rna/running-dragen-on-hpc/installation-and-setup.md) - [FASTQ Processing](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-methods/fastq-processing.md) - [Transcript Counting](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-methods/transcript-counting.md) - [PIPseq CRISPR Mode](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-methods/pipseq-crispr-mode.md) - [Guide RNA Calling](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-methods/guide-rna-calling.md) - [Accessing Results](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/accessing-results.md) - [DRAGEN Report](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report.md) - [Single-Cell RNA](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report/single-cell-rna.md) - [Single-Cell Clustering](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report/single-cell-clustering.md) - [Trimmer](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report/trimmer.md) - [DRAGEN FastQC](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report/dragen-fastqc.md) - [Mapping](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/dragen-report/mapping.md) - [Secondary Analysis Results](https://help.connected.illumina.com/dragen-single-cell-rna/analysis-results/secondary-analysis-results.md) - [Third-party CRISPR Guide Assignment Toolkit](https://help.connected.illumina.com/dragen-single-cell-rna/tertiary-analysis/third-party-crispr-guide-assignment-toolkit.md): Peer-Reviewed Option for performing CRISPR gRNA thresholding - [Illumina Connected Multiomics](https://help.connected.illumina.com/dragen-single-cell-rna/tertiary-analysis/illumina-connected-multiomics.md): Illumina Connected Multiomics (ICM) is available for further tertiary analysis of single-cell and other multiomic data. - [Troubleshooting](https://help.connected.illumina.com/dragen-single-cell-rna/reference/troubleshooting.md) - [FAQ](https://help.connected.illumina.com/dragen-single-cell-rna/reference/faq.md) ## Illumina Connected Multiomics - [About Connected Multiomics](https://help.connected.illumina.com/icm/about/readme.md) - [Interactive Demos](https://help.connected.illumina.com/icm/about/interactive-demos.md) - [Getting Started](https://help.connected.illumina.com/icm/introduction/icm.md) - [Data Inputs](https://help.connected.illumina.com/icm/introduction/upload-data-files.md) - [Transfer Partek Flow Project](https://help.connected.illumina.com/icm/introduction/transfer-partek-flow-project.md) - [Create Study](https://help.connected.illumina.com/icm/studies/create-study.md) - [Add Data](https://help.connected.illumina.com/icm/studies/create-study/add-data.md) - [View Studies](https://help.connected.illumina.com/icm/studies/view-studies.md) - [Samples](https://help.connected.illumina.com/icm/studies/view-studies/view-studies.md) - [Sample Metadata](https://help.connected.illumina.com/icm/studies/view-studies/sample-metadata.md) - [Cell metadata](https://help.connected.illumina.com/icm/studies/view-studies/sample-metadata/cell-metadata.md) - [Sample Groups](https://help.connected.illumina.com/icm/studies/view-studies/view-studies-1.md) - [Analysis and Data Management](https://help.connected.illumina.com/icm/studies/view-studies/view-studies-2.md) - [Study Settings](https://help.connected.illumina.com/icm/studies/view-studies/view-studies-3.md) - [View Analyses Across Studies](https://help.connected.illumina.com/icm/analyses/view-analyses-across-studies.md) - [Enter Analysis](https://help.connected.illumina.com/icm/analyses/enter-analysis.md) - [Analysis Functionality](https://help.connected.illumina.com/icm/analyses/analysis-functionality.md) - [Task Menu](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu.md) - [AI analysis methods summary](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/ai-analysis-methods-summary.md) - [AI analysis suggestions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/ai-analysis-suggestions.md): Provides AI-powered recommendations for the next analysis step based on your current data. - [Task actions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/task-actions.md) - [Data summary report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/data-summary-report.md) - [QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc.md) - [Feature distribution](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/feature-distribution.md) - [Imported count matrix report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/feature-distribution-1.md) - [Single-cell QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/single-cell-qa-qc.md) - [Cell barcode QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/cell-barcode-qa-qc.md) - [5-base Methylation QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/5-base-methylation-qc.md) - [Annotation/Metadata](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata.md) - [Annotate cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells.md) - [Annotate features](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells-1.md) - [Publish cell attributes to project](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/publish-cell-attributes-to-project.md) - [Attribute report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells-2.md) - [Pre-analysis tools](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools.md) - [Pseudobulk](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/pool-cells.md) - [Split by feature type](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/split-matrix.md) - [Generate group cell counts](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-group-cell-counts.md) - [Merge matrices](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/merge-matrices.md) - [Spot clean](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/spot-clean.md) - [Hashtag demultiplexing](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/hashtag-demultiplexing.md) - [Generate beta value](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-beta-value.md) - [Generate methylation mvalues](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-methylation-mvalues.md) - [Filtering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering.md) - [Filter features](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-features.md) - [Filter samples/cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-groups-samples-or-cells.md) - [Filter barcodes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-barcodes.md) - [Split by attribute](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/split-by-attribute.md) - [Downsample cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/downsample-cells.md) - [Normalization and scaling](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling.md) - [Normalization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalization.md) - [Normalize to housekeeping genes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalize-to-housekeeping-genes.md) - [Normalize to baseline](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalize-to-baseline.md) - [Scran deconvolution](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/scran-deconvolution.md) - [TF-IDF normalization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/tf-idf-normalization.md) - [Impute missing values](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/impute-missing-values.md) - [Impute low expression](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/impute-low-expression.md) - [SCTransform](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/sctransform.md) - [Batch removal](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal.md) - [General linear model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/general-linear-model.md) - [Harmony](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/harmony.md) - [Seurat3 integration](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/seurat3-integration.md) - [Statistics](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics.md) - [Differential analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis.md) - [DESeq2](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/deseq2-r-vs-deseq2.md) - [Hurdle model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/hurdle-model.md) - [ANOVA/LIMMA-trend/LIMMA-voom](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/anova-limma-trend-limma-voom.md) - [Welch's ANOVA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/kruskal-wallis.md) - [Kruskal-Wallis / Wilcoxon](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/kruskal-wallis-1.md) - [Detect alt-splicing (ANOVA)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/detect-alt-splicing-anova.md) - [Poisson/Negative binomial/GSA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/gsa.md) - [Transcript Expression Analysis - Cuffdiff](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/transcript-expression-analysis-cuffdiff.md) - [Troubleshooting](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/troubleshooting.md) - [Descriptive statistics](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis.md) - [Correlation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis-1.md) - [QTL analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis-1-1.md) - [Differential methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-methylation.md) - [Detect differential methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/detect-differential-methylation.md) - [Compute biomarkers](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/compute-biomarkers.md) - [Survival Analysis with Cox regression and Kaplan-Meier analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/survival-analysis-with-cox-regression-and-kaplan-meier-analysis.md) - [Classification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/survival-analysis-with-cox-regression-and-kaplan-meier-analysis-1.md) - [Spatially Variable Genes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/spatially-variable-genes.md) - [Exploratory analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis.md) - [Graph-based clustering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/graph-based-clustering.md) - [K-means clustering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/k-means-clustering.md) - [Compare clusters](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/compare-clusters.md) - [PCA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/pca.md) - [t-SNE](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/t-sne.md) - [UMAP](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/umap.md) - [Hierarchical clustering / heatmap](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/hierarchical-clustering.md) - [AUCell](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/aucell.md) - [Find multimodal neighbors](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/find-multimodal-neighbors.md) - [SVD](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/svd.md) - [CellPhoneDB](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/cellphonedb.md) - [BANKSY - Spatial Domain Identification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/banksy-spatial-domain-identification.md) - [Merge differential expression results](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/merge-differential-expression-results.md) - [Region analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis.md) - [Get Regional Methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis/get-regional-methylation.md) - [Annotate Regions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis/annotate-regions.md) - [Trajectory analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis.md) - [Monocle 2](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis/trajectory-analysis-monocle-2.md) - [Monocle 3](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis/trajectory-analysis-monocle-3.md) - [Variant Analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis.md) - [Fusion Gene Detection](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/fusion-gene-detection.md) - [Annotate Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants.md) - [Annotate Variants (SnpEff)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-snpeff.md) - [Annotate Variants (VEP)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-vep.md) - [Filter Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/filter-variants.md) - [Summarize Cohort Mutations](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/summarize-cohort-mutations.md) - [Combine Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/combine-variants.md) - [Filter Variants With Databases](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/filter-variants-with-databases.md) - [Create genotype matrix](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/create-genotype-matrix.md) - [Combine multiomics data](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/combine-multiomics-data.md) - [Combine 5-base methylation and variant data](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/combine-multiomics-data/combine-5-base-methylation-and-variant-data.md) - [Motif Detection](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/motif-detection.md) - [Biological interpretation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation.md) - [Gene Set Enrichment](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gene-set-enrichment.md) - [GSEA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gsea.md) - [Gene set ANOVA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gsea-1.md) - [Correlation Engine atlases](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/correlation-engine-atlases.md) - [Correlation Engine pathways](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/correlation-engine-pathways.md) - [Get targeted mRNA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/get-targeted-mrna.md) - [Classification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification.md) - [Classify cell type](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/classify-cell-type.md) - [Train classifier](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/train-classifier.md) - [ScType](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/sctype.md) - [Conversion](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/conversion.md) - [Region analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis-1.md) - [Annotate regions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis-1/annotate-regions.md) - [Pipelines](https://help.connected.illumina.com/icm/analyses/analysis-functionality/pipelines.md) - [Share Analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/share-analysis.md) - [Data Viewer](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer.md) - [Chromosome View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view.md) - [Launching the Chromosome View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/launching-the-chromosome-view.md) - [Navigating Through the View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/navigating-through-the-view.md) - [Selecting Data Tracks for Visualization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/selecting-data-tracks-for-visualization.md) - [Visualizing the Results Using Data Tracks](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/visualizing-the-results-using-data-tracks.md) - [Annotating the Results](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/annotating-the-results.md) - [Customizing the View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/customizing-the-view.md) - [Dot Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/dot-plot.md) - [Stacked Violin Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/stacked-violin-plot.md) - [Volcano Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/volcano-plot.md) - [Manhattan Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/manhattan-plot.md) - [Venn Diagram](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/list-generator-venn-diagram.md) - [Sources of variation plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/sources-of-variation-plot.md) - [Interaction Plots](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/interaction-plots.md) - [Correlation Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/correlation-plot.md) - [Pie Chart](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/pie-chart.md) - [Sankey Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/pie-chart-1.md) - [Histograms](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/histograms.md) - [Settings](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings.md) - [Lists](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/lists.md) - [Pipeline management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/pipeline-management.md) - [Library File Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management.md) - [Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/library-file-management-page.md) - [Selecting an Assembly](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/selecting-an-assembly.md) - [Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/library-files.md) - [Update Library Index](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/update-library-index.md) - [Creating an Assembly on the Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/creating-an-assembly-on-the-library-file-management-page.md) - [Adding Library Files on the Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-library-files-on-the-library-file-management-page.md) - [Adding a Reference Sequence](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-reference-sequence.md) - [Adding a Cytoband](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-cytoband.md) - [Adding a Gene Set](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-gene-set.md) - [Adding a Variant Annotation Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-variant-annotation-database.md) - [Adding a SnpEff Variant Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-snpeff-variant-database.md) - [Adding a Variant Effect Predictor (VEP) Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-variant-effect-predictor-vep-database.md) - [Adding an Annotation Model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-an-annotation-model.md) - [Adding Library Files from Within a Project](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-library-files-from-within-a-project.md) - [Microarray Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/microarray-library-files.md) - [Removing Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/removing-library-files.md) - [Option Set Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/option-set-management.md) - [Task Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/task-management.md) - [Filter Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/filter-management.md) - [Walkthrough](https://help.connected.illumina.com/icm/analyses/walkthroughs.md) - [Correlation Engine for Gene Discovery](https://help.connected.illumina.com/icm/analyses/walkthroughs/correlation-engine-for-gene-discovery.md): This tutorial walks you through how to export differentially expressed genes or proteins from Connected Multiomics and upload them into Correlation Engine (CE) for deeper biological interpretation. - [Bulk RNA](https://help.connected.illumina.com/icm/analyses/walkthroughs/bulk-rna.md) - [Methylation Array](https://help.connected.illumina.com/icm/analyses/walkthroughs/methylation-array.md) - [Multiomics: miRNA & RNA](https://help.connected.illumina.com/icm/analyses/walkthroughs/multiomics-mirna-and-rna.md) - [Perturb-seq](https://help.connected.illumina.com/icm/analyses/walkthroughs/perturb-seq.md) - [View Samples Across Studies](https://help.connected.illumina.com/icm/global-samples/view-sample-groups-across-studies.md) - [Software Release Notes](https://help.connected.illumina.com/icm/reference/software-release-notes.md) - [Known Limitations](https://help.connected.illumina.com/icm/reference/known-limitations.md) - [How-to Videos and Webinars](https://help.connected.illumina.com/icm/reference/how-to-videos.md) - [Supported Data Types](https://help.connected.illumina.com/icm/reference/supported-data-types.md): The following Illumina and third-party data types are supported in Connected Multiomics: - [iCredits](https://help.connected.illumina.com/icm/reference/icredits.md) - [How to Cite Software](https://help.connected.illumina.com/icm/reference/how-to-cite-software.md) ## Partek - [Overview](https://help.connected.illumina.com/partek/readme.md) - [Partek Flow](https://help.connected.illumina.com/partek/partek-flow.md) - [Frequently Asked Questions](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions.md) - [General](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions/general.md) - [Visualization](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions/visualization.md) - [Statistics](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions/statistics.md) - [Biological Interpretation](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions/biological-interpretation.md) - [How to cite Partek software](https://help.connected.illumina.com/partek/partek-flow/frequently-asked-questions/how-to-cite-partek-software.md) - [Quick Start Guide](https://help.connected.illumina.com/partek/partek-flow/quick-start-guide.md) - [Getting Started with Your Partek Flow Hosted Trial](https://help.connected.illumina.com/partek/partek-flow/quick-start-guide/getting-started-with-your-partek-flow-hosted-trial.md) - [Installation Guide](https://help.connected.illumina.com/partek/partek-flow/installation-guide.md) - [Minimum System Requirements](https://help.connected.illumina.com/partek/partek-flow/installation-guide/minimum-system-requirements.md) - [Single Cell Toolkit System Requirements](https://help.connected.illumina.com/partek/partek-flow/installation-guide/single-cell-toolkit-system-requirements.md) - [Single Node Installation](https://help.connected.illumina.com/partek/partek-flow/installation-guide/single-node-installation.md) - [Installing on Linux](https://help.connected.illumina.com/partek/partek-flow/installation-guide/single-node-installation/installing-on-linux.md) - [Single Node Amazon Web Services Deployment](https://help.connected.illumina.com/partek/partek-flow/installation-guide/single-node-amazon-web-services-deployment.md) - [Multi-Node Cluster Installation](https://help.connected.illumina.com/partek/partek-flow/installation-guide/multi-node-cluster-installation.md) - [Creating Restricted User Folders within the Partek Flow server](https://help.connected.illumina.com/partek/partek-flow/installation-guide/creating-restricted-user-folders-within-the-partek-flow-server.md) - [Updating Partek Flow](https://help.connected.illumina.com/partek/partek-flow/installation-guide/updating-partek-flow.md) - [Uninstalling Partek Flow](https://help.connected.illumina.com/partek/partek-flow/installation-guide/uninstalling-partek-flow.md) - [Dependencies](https://help.connected.illumina.com/partek/partek-flow/installation-guide/dependencies.md) - [Docker and Docker-compose](https://help.connected.illumina.com/partek/partek-flow/installation-guide/docker-and-docker-compose.md) - [Java KeyStore and Certificates](https://help.connected.illumina.com/partek/partek-flow/installation-guide/java-keystore-and-certificates.md) - [Kubernetes](https://help.connected.illumina.com/partek/partek-flow/installation-guide/kubernetes.md) - [Live Training Event Recordings](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings.md) - [Bulk RNA-Seq Analysis Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/bulk-rna-seq-analysis-training.md) - [Basic scRNA-Seq Analysis & Visualization Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/basic-scrna-seq-analysis-and-visualization-training.md) - [Advanced scRNA-Seq Data Analysis Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/advanced-scrna-seq-data-analysis-training.md) - [Bulk RNA-Seq and ATAC-Seq Integration Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/bulk-rna-seq-and-atac-seq-integration-training.md) - [Spatial Transcriptomics Data Analysis Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/spatial-transcriptomics-data-analysis-training.md) - [scRNA and scATAC Data Integration Training](https://help.connected.illumina.com/partek/partek-flow/live-training-event-recordings/scrna-and-scatac-data-integration-training.md) - [Tutorials](https://help.connected.illumina.com/partek/partek-flow/tutorials.md) - [Creating and Analyzing a Project](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project.md) - [Creating a New Project](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/creating-a-new-project.md) - [The Metadata Tab](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-metadata-tab.md) - [The Analyses Tab](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-analyses-tab.md) - [The Log Tab](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-log-tab.md) - [The Project Settings Tab](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-project-settings-tab.md) - [The Attachments Tab](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-attachments-tab.md) - [Project Management](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/project-management.md) - [Importing a GEO / ENA project](https://help.connected.illumina.com/partek/partek-flow/tutorials/creating-and-analyzing-a-project/importing-a-geo-ena-project.md) - [Bulk RNA-Seq](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq.md) - [Importing the tutorial data set](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/importing-the-tutorial-data-set.md) - [Adding sample attributes](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/adding-sample-attributes.md) - [Running pre-alignment QA/QC](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/running-pre-alignment-qa-qc.md) - [Trimming bases and filtering reads](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/trimming-bases-and-filtering-reads.md) - [Aligning to a reference genome](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/aligning-to-a-reference-genome.md) - [Running post-alignment QA/QC](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/running-post-alignment-qa-qc.md) - [Quantifying to an annotation model](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/quantifying-to-an-annotation-model.md) - [Filtering features](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/filtering-features.md) - [Normalizing counts](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/normalizing-counts.md) - [Exploring the data set with PCA](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/exploring-the-data-set-with-pca.md) - [Performing differential expression analysis with DESeq2](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/performing-differential-expression-analysis-with-deseq2.md) - [Viewing DESeq2 results and creating a gene list](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/viewing-deseq2-results-and-creating-a-gene-list.md) - [Viewing a dot plot for a gene](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/viewing-a-dot-plot-for-a-gene.md) - [Visualizing gene expression in Chromosome view](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/visualizing-gene-expression-in-chromosome-view.md) - [Generating a hierarchical clustering heatmap](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/generating-a-hierarchical-clustering-heatmap.md) - [Performing biological interpretation](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/performing-biological-interpretation.md) - [Saving and running a pipeline](https://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/saving-and-running-a-pipeline.md) - [Analyzing Single Cell RNA-Seq Data](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-single-cell-rna-seq-data.md) - [Analyzing CITE-Seq Data](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data.md) - [Importing Feature Barcoding Data](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data/importing-feature-barcoding-data.md) - [Data Processing](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data/data-processing.md) - [Dimensionality Reduction and Clustering](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data/dimensionality-reduction-and-clustering.md) - [Classifying Cells](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data/classifying-cells.md) - [Differentially Expressed Proteins and Genes](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-cite-seq-data/differentially-expressed-proteins-and-genes.md) - [10x Genomics Visium Spatial Data Analysis](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis.md) - [Start with pre-processed Space Ranger output files](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-pre-processed-space-ranger-output-files.md) - [Start with 10x Genomics Visium fastq files](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-10x-genomics-visium-fastq-files.md) - [Spatial data analysis steps](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/spatial-data-analysis-steps.md) - [View tissue images](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/view-tissue-images.md) - [10x Genomics Xenium Data Analysis](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis.md) - [Import 10x Genomics Xenium Analyzer output](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/import-10x-genomics-xenium-analyzer-output.md) - [Process Xenium data](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/process-xenium-data.md) - [Perform Exploratory analysis](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/perform-exploratory-analysis.md) - [Make comparisons using Compute biomarkers and Biological interpretation](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/make-comparisons-using-compute-biomarkers-and-biological-interpretation.md) - [Single Cell RNA-Seq Analysis (Multiple Samples)](https://help.connected.illumina.com/partek/partek-flow/tutorials/single-cell-rna-seq-analysis-multiple-samples.md) - [Getting started with the tutorial data set](https://help.connected.illumina.com/partek/partek-flow/tutorials/single-cell-rna-seq-analysis-multiple-samples/getting-started-with-the-tutorial-data-set.md) - [Classify cells from multiple samples using t-SNE](https://help.connected.illumina.com/partek/partek-flow/tutorials/single-cell-rna-seq-analysis-multiple-samples/classify-cells-from-multiple-samples-using-t-sne.md) - [Compare expression between cell types with multiple samples](https://help.connected.illumina.com/partek/partek-flow/tutorials/single-cell-rna-seq-analysis-multiple-samples/compare-expression-between-cell-types-with-multiple-samples.md) - [Analyzing Single Cell ATAC-Seq data](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-single-cell-atac-seq-data.md) - [Analyzing Illumina Infinium Methylation array data](https://help.connected.illumina.com/partek/partek-flow/tutorials/analyzing-illumina-infinium-methylation-array-data.md) - [NanoString CosMx Tutorial](https://help.connected.illumina.com/partek/partek-flow/tutorials/nanostring-cosmx-tutorial.md) - [Importing CosMx data](https://help.connected.illumina.com/partek/partek-flow/tutorials/nanostring-cosmx-tutorial/importing-cosmx-data.md) - [QA/QC, data processing, and dimension reduction](https://help.connected.illumina.com/partek/partek-flow/tutorials/nanostring-cosmx-tutorial/qa-qc-data-processing-and-dimension-reduction.md) - [Cell typing](https://help.connected.illumina.com/partek/partek-flow/tutorials/nanostring-cosmx-tutorial/cell-typing.md) - [Classify subpopulations & differential expression analysis](https://help.connected.illumina.com/partek/partek-flow/tutorials/nanostring-cosmx-tutorial/classify-subpopulations-and-differential-expression-analysis.md) - [User Manual](https://help.connected.illumina.com/partek/partek-flow/user-manual.md) - [Interface](https://help.connected.illumina.com/partek/partek-flow/user-manual/interface.md) - [Importing Data](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data.md) - [SFTP File Transfer Instructions](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/sftp-file-transfer-instructions.md) - [Import single cell data](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/import-single-cell-data.md) - [Importing 10x Genomics Matrix Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/importing-10x-genomics-matrix-files.md) - [Importing and Demultiplexing Illumina BCL Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/importing-and-demultiplexing-illumina-bcl-files.md) - [Partek Flow Uploader for Ion Torrent](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/partek-flow-uploader-for-ion-torrent.md) - [Importing 10x Genomics .bcl Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/importing-10x-genomics-bcl-files.md) - [Import a GEO / ENA project](https://help.connected.illumina.com/partek/partek-flow/user-manual/importing-data/import-a-geo-ena-project.md) - [Task Menu](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu.md) - [Task actions](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/task-actions.md) - [Data summary report](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/data-summary-report.md) - [QA/QC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc.md) - [Pre-alignment QA/QC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/pre-alignment-qa-qc.md) - [ERCC Assessment](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/ercc-assessment.md) - [Post-alignment QA/QC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/post-alignment-qa-qc.md) - [Coverage Report](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/coverage-report.md) - [Validate Variants](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/validate-variants.md) - [Feature distribution](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/feature-distribution.md) - [Single-cell QA/QC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/single-cell-qa-qc.md) - [Cell barcode QA/QC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/qa-qc/cell-barcode-qa-qc.md) - [Pre-alignment tools](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-alignment-tools.md) - [Trim bases](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-bases.md) - [Trim adapters](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-adapters.md) - [Filter reads](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/filter-reads.md) - [Trim tags](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-tags.md) - [Post-alignment tools](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools.md) - [Filter alignments](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools/filter-alignments.md) - [Convert alignments to unaligned reads](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools/convert-alignments-to-unaligned-reads.md) - [Combine alignments](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools/combine-alignments.md) - [Deduplicate UMIs](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools/deduplicate-umis.md) - [Downscale alignments](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/post-alignment-tools/downscale-alignments.md) - [Annotation/Metadata](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata.md) - [Annotate cells](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotate-cells.md) - [Annotation report](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotation-report.md) - [Publish cell attributes to project](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/publish-cell-attributes-to-project.md) - [Attribute report](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/attribute-report.md) - [Annotate Visium image](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotate-visium-image.md) - [Pre-analysis tools](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools.md) - [Generate group cell counts](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/generate-group-cell-counts.md) - [Pool cells](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/pool-cells.md) - [Split matrix](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/split-matrix.md) - [Hashtag demultiplexing](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/hashtag-demultiplexing.md) - [Merge matrices](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/merge-matrices.md) - [Descriptive statistics](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/descriptive-statistics.md) - [Spot clean](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/spot-clean.md) - [Aligners](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/aligners.md) - [Quantification](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification.md) - [Quantify to annotation model (Partek E/M)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-annotation-model-partek-em.md) - [Quantify to transcriptome (Cufflinks)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-transcriptome-cufflinks.md) - [Quantify to reference (Partek E/M)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-reference-partek-em.md) - [Quantify regions](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-regions.md) - [HTSeq](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/htseq.md) - [Count feature barcodes](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/count-feature-barcodes.md) - [Salmon](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/salmon.md) - [Filtering](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering.md) - [Filter features](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering/filter-features.md) - [Filter groups (samples or cells)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering/filter-groups-samples-or-cells.md) - [Filter barcodes](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering/filter-barcodes.md) - [Split by attribute](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering/split-by-attribute.md) - [Downsample Cells](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/filtering/downsample-cells.md) - [Normalization and scaling](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling.md) - [Impute low expression](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/impute-low-expression.md) - [Impute missing values](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/impute-missing-values.md) - [Normalization](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalization.md) - [Normalize to baseline](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalize-to-baseline.md) - [Normalize to housekeeping genes](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalize-to-housekeeping-genes.md) - [Scran deconvolution](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/scran-deconvolution.md) - [SCTransform](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/sctransform.md) - [TF-IDF normalization](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/tf-idf-normalization.md) - [Batch removal](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/batch-removal.md) - [General linear model](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/batch-removal/general-linear-model.md) - [Harmony](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/batch-removal/harmony.md) - [Seurat3 integration](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/batch-removal/seurat3-integration.md) - [Differential Analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis.md) - [GSA](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/gsa.md) - [ANOVA/LIMMA-trend/LIMMA-voom](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/anova-limma-trend-limma-voom.md) - [Kruskal-Wallis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/kruskal-wallis.md) - [Detect alt-splicing (ANOVA)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/detect-alt-splicing-anova.md) - [DESeq2(R) vs DESeq2](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/deseq2-r-vs-deseq2.md) - [Hurdle model](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/hurdle-model.md) - [Compute biomarkers](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/compute-biomarkers.md) - [Transcript Expression Analysis - Cuffdiff](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/transcript-expression-analysis-cuffdiff.md) - [Troubleshooting](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/troubleshooting.md) - [Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/survival-analysis-with-cox-regression-and-kaplan-meier-analysis-partek-flow.md) - [Exploratory Analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis.md) - [Graph-based Clustering](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/graph-based-clustering.md) - [K-means Clustering](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/k-means-clustering.md) - [Compare Clusters](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/compare-clusters.md) - [PCA](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/pca.md) - [t-SNE](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/t-sne.md) - [UMAP](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/umap.md) - [Hierarchical Clustering](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/hierarchical-clustering.md) - [AUCell](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/aucell.md) - [Find multimodal neighbors](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/find-multimodal-neighbors.md) - [SVD](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/svd.md) - [CellPhoneDB](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/exploratory-analysis/cellphonedb.md) - [Trajectory Analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/trajectory-analysis.md) - [Trajectory Analysis (Monocle 2)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-2.md) - [Trajectory Analysis (Monocle 3)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-3.md) - [Variant Callers](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-callers.md) - [SAMtools](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-callers/samtools.md) - [FreeBayes](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-callers/freebayes.md) - [LoFreq](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-callers/lofreq.md) - [Variant Analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis.md) - [Fusion Gene Detection](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/fusion-gene-detection.md) - [Annotate Variants](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants.md) - [Annotate Variants (SnpEff)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants-snpeff.md) - [Annotate Variants (VEP)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants-vep.md) - [Filter Variants](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/filter-variants.md) - [Summarize Cohort Mutations](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/summarize-cohort-mutations.md) - [Combine Variants](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/variant-analysis/combine-variants.md) - [Copy Number Analysis (CNVkit)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/copy-number-analysis-cnvkit.md) - [Peak Callers (MACS2)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/peak-callers-macs2.md) - [Peak analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/peak-analysis.md) - [Annotate Peaks](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/peak-analysis/annotate-peaks.md) - [Filter peaks](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/peak-analysis/filter-peaks.md) - [Promoter sum matrix](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/peak-analysis/promoter-sum-matrix.md) - [Motif Detection](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/motif-detection.md) - [Metagenomics](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/metagenomics.md) - [Kraken](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/metagenomics/kraken.md) - [Alpha & beta diversity](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/metagenomics/alpha-and-beta-diversity.md) - [Choose taxonomic level](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/metagenomics/choose-taxonomic-level.md) - [10x Genomics](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/10x-genomics.md) - [Cell Ranger - Gene Expression](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/10x-genomics/cell-ranger-gene-expression.md) - [Cell Ranger - ATAC](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/10x-genomics/cell-ranger-atac.md) - [Space Ranger](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/10x-genomics/space-ranger.md) - [STARsolo](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/10x-genomics/starsolo.md) - [V(D)J Analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/vdj-analysis.md) - [Biological Interpretation](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation.md) - [Gene Set Enrichment](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation/gene-set-enrichment.md) - [GSEA](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation/gsea.md) - [Correlation](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/correlation.md) - [Correlation analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/correlation/correlation-analysis.md) - [Sample Correlation](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/correlation/sample-correlation.md) - [Similarity matrix](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/correlation/similarity-matrix.md) - [Export](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/export.md) - [Classification](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/classification.md) - [Feature linkage analysis](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/feature-linkage-analysis.md) - [Data Viewer](https://help.connected.illumina.com/partek/partek-flow/user-manual/data-viewer.md) - [Visualizations](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations.md) - [Chromosome View](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view.md) - [Launching the Chromosome View](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/launching-the-chromosome-view.md) - [Navigating Through the View](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/navigating-through-the-view.md) - [Selecting Data Tracks for Visualization](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/selecting-data-tracks-for-visualization.md) - [Visualizing the Results Using Data Tracks](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/visualizing-the-results-using-data-tracks.md) - [Annotating the Results](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/annotating-the-results.md) - [Customizing the View](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/chromosome-view/customizing-the-view.md) - [Dot Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/dot-plot.md) - [Volcano Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/volcano-plot.md) - [List Generator (Venn Diagram)](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/list-generator-venn-diagram.md) - [Sankey Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/sankey-plot.md) - [Transcription Start Site (TSS) Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/transcription-start-site-tss-plot.md) - [Sources of variation plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/sources-of-variation-plot.md) - [Interaction Plots](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/interaction-plots.md) - [Correlation Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/correlation-plot.md) - [Pie Chart](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/pie-chart.md) - [Histograms](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/histograms.md) - [Heatmaps](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/heatmaps.md) - [PCA, UMAP and tSNE scatter plots](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/pca-umap-and-tsne-scatter-plots.md) - [Stacked Violin Plot](https://help.connected.illumina.com/partek/partek-flow/user-manual/visualizations/stacked-violin-plot.md) - [Pipelines](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines.md) - [Making a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/making-a-pipeline.md) - [Running a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/running-a-pipeline.md) - [Downloading and Sharing a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/downloading-and-sharing-a-pipeline.md) - [Previewing a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/previewing-a-pipeline.md) - [Deleting a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/deleting-a-pipeline.md) - [Importing a Pipeline](https://help.connected.illumina.com/partek/partek-flow/user-manual/pipelines/importing-a-pipeline.md) - [Large File Viewer](https://help.connected.illumina.com/partek/partek-flow/user-manual/large-file-viewer.md) - [Settings](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings.md) - [Personal](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/personal.md) - [My Profile](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/personal/my-profile.md) - [My Preferences](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/personal/my-preferences.md) - [Forgot Password](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/personal/forgot-password.md) - [System](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/system.md) - [System Information](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/system/system-information.md) - [System Preferences](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/system/system-preferences.md) - [LDAP Configuration](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/system/ldap-configuration.md) - [Components](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components.md) - [Filter Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/filter-management.md) - [Library File Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management.md) - [Library File Management Settings](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/library-file-management-settings.md) - [Library File Management Page](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/library-file-management-page.md) - [Selecting an Assembly](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/selecting-an-assembly.md) - [Library Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/library-files.md) - [Update Library Index](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/update-library-index.md) - [Creating an Assembly on the Library File Management Page](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/creating-an-assembly-on-the-library-file-management-page.md) - [Adding Library Files on the Library File Management Page](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-library-files-on-the-library-file-management-page.md) - [Adding a Reference Sequence](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-reference-sequence.md) - [Adding a Cytoband](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-cytoband.md) - [Adding Reference Aligner Indexes](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-reference-aligner-indexes.md) - [Adding a Gene Set](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-gene-set.md) - [Adding a Variant Annotation Database](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-variant-annotation-database.md) - [Adding a SnpEff Variant Database](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-snpeff-variant-database.md) - [Adding a Variant Effect Predictor (VEP) Database](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-a-variant-effect-predictor-vep-database.md) - [Adding an Annotation Model](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-an-annotation-model.md) - [Adding Aligner Indexes Based on an Annotation Model](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-aligner-indexes-based-on-an-annotation-model.md) - [Adding Library Files from Within a Project](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-library-files-from-within-a-project.md) - [Microarray Library Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/microarray-library-files.md) - [Adding Prep kit](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/adding-prep-kit.md) - [Removing Library Files](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/library-file-management/removing-library-files.md) - [Option Set Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/option-set-management.md) - [Task Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/task-management.md) - [Pipeline managment](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/pipeline-management.md) - [Lists](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/lists.md) - [Access](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access.md) - [User Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/user-management.md) - [Group Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/group-management.md) - [Licensing](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/licensing.md) - [Directory Permissions](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/directory-permissions.md) - [Access Control Log](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/access-control-log.md) - [Failed Logins](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/failed-logins.md) - [Orphaned files](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/access/orphaned-files.md) - [Usage](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/usage.md) - [System Queue](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/usage/system-queue.md) - [System Resources](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/usage/system-resources.md) - [Usage Report](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/usage/usage-report.md) - [Server Management](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management.md) - [Backing Up the Database](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management/backing-up-the-database.md) - [System Administrator Guide (Linux)](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management/system-administrator-guide-linux.md) - [Diagnosing Issues](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management/diagnosing-issues.md) - [Moving Data](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management/moving-data.md) - [Partek Flow Worker Allocator](https://help.connected.illumina.com/partek/partek-flow/user-manual/server-management/partek-flow-worker-allocator.md) - [Enterprise Features and Toolkits](https://help.connected.illumina.com/partek/partek-flow/user-manual/enterprise-features-and-toolkits.md) - [REST API](https://help.connected.illumina.com/partek/partek-flow/user-manual/enterprise-features-and-toolkits/rest-api.md) - [REST API Command List](https://help.connected.illumina.com/partek/partek-flow/user-manual/enterprise-features-and-toolkits/rest-api/rest-api-command-list.md) - [Microarray Toolkit](https://help.connected.illumina.com/partek/partek-flow/user-manual/microarray-toolkit.md) - [Importing Custom Microarrays](https://help.connected.illumina.com/partek/partek-flow/user-manual/microarray-toolkit/importing-custom-microarrays.md) - [Glossary](https://help.connected.illumina.com/partek/partek-flow/user-manual/glossary.md) - [Partek Flow FAQs](https://help.connected.illumina.com/partek/partek-flow/user-manual/partek-flow-faqs.md) - [Webinars](https://help.connected.illumina.com/partek/partek-flow/webinars.md) - [Blog Posts](https://help.connected.illumina.com/partek/partek-flow/blog-posts.md) - [How to select the best single cell quality control thresholds](https://help.connected.illumina.com/partek/partek-flow/blog-posts/how-to-select-the-best-single-cell-quality-control-thresholds.md) - [Cellular Differentiation Using Trajectory Analysis & Single Cell RNA-Seq Data](https://help.connected.illumina.com/partek/partek-flow/blog-posts/using-trajectory-analysis-to-study-cellular-differentiation-in-single-cell-rna-seq-experiments.md) - [Spatial transcriptomics—what’s the big deal and why you should do it](https://help.connected.illumina.com/partek/partek-flow/blog-posts/spatial-transcriptomics-whats-the-big-deal-and-why-you-should-do-it.md) - [Detecting differential gene expression in single cell RNA-Seq analysis](https://help.connected.illumina.com/partek/partek-flow/blog-posts/less-is-more-detecting-differential-gene-expression-in-single-cell-rna-seq-analysis.md) - [Batch remover for single cell data](https://help.connected.illumina.com/partek/partek-flow/blog-posts/batch-remover-for-single-cell-data.md) - [How to perform single cell RNA sequencing: exploratory analysis](https://help.connected.illumina.com/partek/partek-flow/blog-posts/how-to-perform-single-cell-rna-sequencing-exploratory-analysis.md) - [Single Cell Multiomics Analysis: Strategies for Integration](https://help.connected.illumina.com/partek/partek-flow/blog-posts/single-cell-multiomics-analysis-strategies-for-integration.md) - [Pathway Analysis: ANOVA vs. Enrichment Analysis](https://help.connected.illumina.com/partek/partek-flow/blog-posts/pathway-analysis-anova-vs.-enrichment-analysis.md) - [Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein](https://help.connected.illumina.com/partek/partek-flow/blog-posts/studying-immunotherapy-with-multimodal-omics-simultaneous-measurement-of-gene-and-protein.md) - [How to Integrate ChIP-Seq and RNA-Seq Data](https://help.connected.illumina.com/partek/partek-flow/blog-posts/how-to-integrate-chip-seq-and-rna-seq-data.md) - [Enjoy Responsibly!](https://help.connected.illumina.com/partek/partek-flow/blog-posts/enjoy-responsibly.md) - [To Boldly Go…](https://help.connected.illumina.com/partek/partek-flow/blog-posts/to-boldly-go....md) - [Get to Know Your Cell](https://help.connected.illumina.com/partek/partek-flow/blog-posts/get-to-know-your-cell.md) - [Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow](https://help.connected.illumina.com/partek/partek-flow/blog-posts/aliens-among-us-how-i-analyzed-non-model-organism-data-in-partek-flow.md) - [White Papers](https://help.connected.illumina.com/partek/partek-flow/white-papers.md) - [Understanding Reads in RNA-Seq Analysis](https://help.connected.illumina.com/partek/partek-flow/white-papers/understanding-reads-in-rna-seq-analysis.md) - [RNA-Seq Quantification](https://help.connected.illumina.com/partek/partek-flow/white-papers/rna-seq-quantification.md) - [Gene-specific Analysis](https://help.connected.illumina.com/partek/partek-flow/white-papers/gene-specific-analysis.md) - [Gene Set ANOVA](https://help.connected.illumina.com/partek/partek-flow/white-papers/gene-set-anova.md) - [Partek Flow Security](https://help.connected.illumina.com/partek/partek-flow/white-papers/partek-flow-security.md) - [Single Cell Scaling](https://help.connected.illumina.com/partek/partek-flow/white-papers/single-cell-scaling.md) - [UMI Deduplication in Partek Flow](https://help.connected.illumina.com/partek/partek-flow/white-papers/umi-deduplication-in-partek-flow.md) - [Mapping error statistics](https://help.connected.illumina.com/partek/partek-flow/white-papers/mapping-error-statistics.md) - [Release Notes](https://help.connected.illumina.com/partek/partek-flow/release-notes.md) - [Release Notes Archive - Partek Flow 10](https://help.connected.illumina.com/partek/partek-flow/release-notes/release-notes-archive-partek-flow-10.md) - [Partek Genomics Suite](https://help.connected.illumina.com/partek/partek-genomics-suite.md) - [Installation Guide](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide.md) - [Minimum System Requirements](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/minimum-system-requirements.md) - [Computer Host ID Retrieval](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/computer-host-id-retrieval.md) - [Node Locked Installation](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/node-locked-installation.md) - [Windows Installation](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/node-locked-installation/windows-installation.md) - [Macintosh Installation](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/node-locked-installation/macintosh-installation.md) - [Floating/Locked Floating Installation](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation.md) - [Linux Installation](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation/linux-installation.md) - [FlexNet Installation on Linux](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation/linux-installation/flexnet-installation-on-linux.md) - [Installing FlexNet on Windows](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation/installing-flexnet-on-windows.md) - [License Server FAQ's](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation/license-server-faqs.md) - [Client Computer Connection to License Server](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/floating-locked-floating-installation/client-computer-connection-to-license-server.md) - [Uninstalling Partek Genomics Suite](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/uninstalling-partek-genomics-suite.md) - [Updating to Version 7.0](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/updating-to-version-7.0.md) - [License Types](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/license-types.md) - [Installation FAQs](https://help.connected.illumina.com/partek/partek-genomics-suite/installation-guide/installation-faqs.md) - [User Manual](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual.md) - [Lists](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists.md) - [Importing a text file list](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/importing-a-text-file-list.md) - [Adding annotations to a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/adding-annotations-to-a-gene-list.md) - [Tasks available for a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/tasks-available-for-a-gene-list.md) - [Starting with a list of genomic regions](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/starting-with-a-list-of-genomic-regions.md) - [Starting with a list of SNPs](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/starting-with-a-list-of-snps.md) - [Importing a BED file](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/importing-a-bed-file.md) - [Additional options for lists](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/lists/additional-options-for-lists.md) - [Annotation](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/annotation.md) - [Hierarchical Clustering Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/hierarchical-clustering-analysis.md) - [Gene Ontology ANOVA](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova.md) - [Implementation Details](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/implementation-details.md) - [Configuring the GO ANOVA Dialog](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/configuring-the-go-anova-dialog.md) - [Performing GO ANOVA](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/performing-go-anova.md) - [GO ANOVA Output](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/go-anova-output.md) - [GO ANOVA Visualisations](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/go-anova-visualisations.md) - [Recommended Filters](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/gene-ontology-anova/recommended-filters.md) - [Visualizations](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations.md) - [Dot Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/dot-plot.md) - [Profile Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/profile-plot.md) - [XY Plot / Bar Chart](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/xy-plot-bar-chart.md) - [Volcano Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/volcano-plot.md) - [Scatter Plot and MA Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/scatter-plot-and-ma-plot.md) - [Sort Rows by Prototype](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/sort-rows-by-prototype.md) - [Manhattan Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/manhattan-plot.md) - [Violin Plot](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizations/violin-plot.md) - [Visualizing NGS Data](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/visualizing-ngs-data.md) - [Chromosome View](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/chromosome-view.md) - [Methylation Workflows](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/methylation-workflows.md) - [Trio/Duo Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/trio-duo-analysis.md) - [Association Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/association-analysis.md) - [LOH detection with an allele ratio spreadsheet](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/loh-detection-with-an-allele-ratio-spreadsheet.md) - [Import data from Agilent feature extraction software](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/import-data-from-agilent-feature-extraction-software.md) - [Illumina GenomeStudio Plugin](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin.md) - [Import gene expression data](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin/import-gene-expression-data.md) - [Import Genotype Data](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin/import-genotype-data.md) - [Export CNV data to Illumina GenomeStudio using Partek report plug-in](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin/export-cnv-data-to-illumina-genomestudio-using-partek-report-plug-in.md) - [Import data from Illumina GenomeStudio using Partek plug-in](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin/import-data-from-illumina-genomestudio-using-partek-plug-in.md) - [Export methylation data to Illumina GenomeStudio using Partek report plug-in](https://help.connected.illumina.com/partek/partek-genomics-suite/user-manual/illumina-genomestudio-plugin/export-methylation-data-to-illumina-genomestudio-using-partek-report-plug-in.md) - [Tutorials](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials.md) - [Gene Expression Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis.md) - [Importing Affymetrix CEL files](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/importing-affymetrix-cel-files.md) - [Adding sample information](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/adding-sample-information.md) - [Exploring gene expression data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/exploring-gene-expression-data.md) - [Identifying differentially expressed genes using ANOVA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/identifying-differentially-expressed-genes-using-anova.md) - [Creating gene lists from ANOVA results](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/creating-gene-lists-from-anova-results.md) - [Performing hierarchical clustering](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/performing-hierarchical-clustering.md) - [Adding gene annotations](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis/adding-gene-annotations.md) - [Gene Expression Analysis with Batch Effects](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects.md) - [Importing the data set](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/importing-the-data-set.md) - [Adding an annotation link](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/adding-an-annotation-link.md) - [Exploring the data set with PCA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/exploring-the-data-set-with-pca.md) - [Detect differentially expressed genes with ANOVA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/detect-differentially-expressed-genes-with-anova.md) - [Removing batch effects](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/removing-batch-effects.md) - [Creating a gene list using the Venn Diagram](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/creating-a-gene-list-using-the-venn-diagram.md) - [Hierarchical clustering using a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/hierarchical-clustering-using-a-gene-list.md) - [GO enrichment using a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/go-enrichment-using-a-gene-list.md) - [Differential Methylation Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis.md) - [Import and normalize methylation data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/import-and-normalize-methylation-data.md) - [Annotate samples](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/annotate-samples.md) - [Perform data quality analysis and quality control](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/perform-data-quality-analysis-and-quality-control.md) - [Detect differentially methylated loci](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/detect-differentially-methylated-loci.md) - [Create a marker list](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/create-a-marker-list.md) - [Filter loci with the interactive filter](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/filter-loci-with-the-interactive-filter.md) - [Obtain methylation signatures](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/obtain-methylation-signatures.md) - [Visualize methylation at each locus](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/visualize-methylation-at-each-locus.md) - [Perform gene set and pathway analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/perform-gene-set-and-pathway-analysis.md) - [Detect differentially methylated CpG islands](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/detect-differentially-methylated-cpg-islands.md) - [Optional: Add UCSC CpG island annotations](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/optional-add-ucsc-cpg-island-annotations.md) - [Optional: Use MethylationEPIC for CNV analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/optional-use-methylationepic-for-cnv-analysis.md) - [Optional: Import a Partek Project from Genome Studio](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/differential-methylation-analysis/optional-import-a-partek-project-from-genome-studio.md) - [Partek Pathway](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/partek-pathway.md) - [Performing pathway enrichment](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/partek-pathway/performing-pathway-enrichment.md) - [Analyzing pathway enrichment in Partek Genomics Suite](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/partek-pathway/analyzing-pathway-enrichment-in-partek-genomics-suite.md) - [Analyzing pathway enrichment in Partek Pathway](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/partek-pathway/analyzing-pathway-enrichment-in-partek-pathway.md) - [Gene Ontology Enrichment](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-ontology-enrichment.md) - [Open a zipped project](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-ontology-enrichment/open-a-zipped-project.md) - [Perform GO enrichment analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-ontology-enrichment/perform-go-enrichment-analysis.md) - [RNA-Seq Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis.md) - [Importing aligned reads](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/importing-aligned-reads.md) - [Adding sample attributes](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/adding-sample-attributes.md) - [RNA-Seq mRNA quantification](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/rna-seq-mrna-quantification.md) - [Detecting differential expression in RNA-Seq data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/detecting-differential-expression-in-rna-seq-data.md) - [Creating a gene list with advanced options](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/creating-a-gene-list-with-advanced-options.md) - [Visualizing mapped reads with Chromosome View](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/visualizing-mapped-reads-with-chromosome-view.md) - [Visualizing differential isoform expression](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/visualizing-differential-isoform-expression.md) - [Gene Ontology (GO) Enrichment](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/gene-ontology-go-enrichment.md) - [Analyzing the unexplained regions spreadsheet](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/rna-seq-analysis/analyzing-the-unexplained-regions-spreadsheet.md) - [ChIP-Seq Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis.md) - [Importing ChIP-Seq data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/importing-chip-seq-data.md) - [Quality control for ChIP-Seq samples](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/quality-control-for-chip-seq-samples.md) - [Detecting peaks and enriched regions in ChIP-Seq data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/detecting-peaks-and-enriched-regions-in-chip-seq-data.md) - [Creating a list of enriched regions](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/creating-a-list-of-enriched-regions.md) - [Identifying novel and known motifs](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/identifying-novel-and-known-motifs.md) - [Finding nearest genomic features](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/finding-nearest-genomic-features.md) - [Visualizing reads and enriched regions](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/chip-seq-analysis/visualizing-reads-and-enriched-regions.md) - [Survival Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/survival-analysis.md) - [Kaplan-Meier Survival Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/survival-analysis/kaplan-meier-survival-analysis.md) - [Cox Regression Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/survival-analysis/cox-regression-analysis.md) - [Model Selection Tool](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/model-selection-tool.md) - [Copy Number Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis.md) - [Importing Copy Number Data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/importing-copy-number-data.md) - [Exploring the data with PCA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/exploring-the-data-with-pca.md) - [Creating Copy Number from Allele Intensities](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/creating-copy-number-from-allele-intensities.md) - [Detecting regions with copy number variation](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/detecting-regions-with-copy-number-variation.md) - [Creating a list of regions](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/creating-a-list-of-regions.md) - [Finding genes with copy number variation](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/finding-genes-with-copy-number-variation.md) - [Optional: Additional options for annotating regions](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/optional-additional-options-for-annotating-regions.md) - [Optional: GC wave correction for Affymetrix CEL files](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/optional-gc-wave-correction-for-affymetrix-cel-files.md) - [Optional: Integrating copy number with LOH and AsCN](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/copy-number-analysis/optional-integrating-copy-number-with-loh-and-ascn.md) - [Loss of Heterozygosity](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/loss-of-heterozygosity.md) - [Allele Specific Copy Number](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/allele-specific-copy-number.md) - [Gene Expression - Aging Study](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-aging-study.md) - [miRNA Expression and Integration with Gene Expression](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/mirna-expression-and-integration-with-gene-expression.md) - [Analyze differentially expressed miRNAs](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/mirna-expression-and-integration-with-gene-expression/analyze-differentially-expressed-mirnas.md) - [Integrate miRNA and Gene Expression data](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/mirna-expression-and-integration-with-gene-expression/integrate-mirna-and-gene-expression-data.md) - [Promoter Tiling Array](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/promoter-tiling-array.md) - [Human Exon Array](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/human-exon-array.md) - [Importing Human Exon Array](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/human-exon-array/importing-human-exon-array.md) - [Gene-level Analysis of Exon Array](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/human-exon-array/gene-level-analysis-of-exon-array.md) - [Alt-Splicing Analysis of Exon Array](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/human-exon-array/alt-splicing-analysis-of-exon-array.md) - [NCBI GEO Importer](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/ncbi-geo-importer.md) - [Webinars](https://help.connected.illumina.com/partek/partek-genomics-suite/webinars.md) - [White Papers](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers.md) - [Allele Intensity Import](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/allele-intensity-import.md) - [Allele-Specific Copy Number](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/allele-specific-copy-number.md) - [Calculating Genotype Likelihoods](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/calculating-genotype-likelihoods.md) - [ChIP-Seq Peak Detection](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/chip-seq-peak-detection.md) - [Detect Regions of Significance](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/detect-regions-of-significance.md) - [Genomic Segmentation](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/genomic-segmentation.md) - [Loss of Heterozygosity Analysis](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/loss-of-heterozygosity-analysis.md) - [Motif Discovery Methods](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/motif-discovery-methods.md) - [Partek Genomics Suite Security](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/partek-genomics-suite-security.md) - [Reads in RNA-Seq](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/reads-in-rna-seq.md) - [RNA-Seq Methods](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/rna-seq-methods.md) - [Unpaired Copy Number Estimation](https://help.connected.illumina.com/partek/partek-genomics-suite/white-papers/unpaired-copy-number-estimation.md) - [Release Notes](https://help.connected.illumina.com/partek/partek-genomics-suite/release-notes.md) - [Version Updates](https://help.connected.illumina.com/partek/partek-genomics-suite/version-updates.md) - [TeamViewer Instructions](https://help.connected.illumina.com/partek/partek-genomics-suite/teamviewer-instructions.md) - [Getting Help](https://help.connected.illumina.com/partek/getting-help.md) - [TeamViewer Instructions](https://help.connected.illumina.com/partek/getting-help/teamviewer-instructions.md) --- # Agent Instructions This documentation is published with GitBook. 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