> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/illumina-trupath-genome/get-started/readme.md). # Introduction Illumina TruPath Genome Software Product Overview ## Introduction Illumina TruPath Genome Software is an end-to-end whole-genome workflow that connects NovaSeq X Sequencing, DRAGEN Germline Secondary Analysis, and Emedgene Interpretation within the Illumina Bioinsight Platform. {% hint style="info" %} **Before you start** * Sequencing requires a NovaSeq X Series instrument with [1.4 Software Package](https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/novaseq-x-series/200079828_00_NovaSeq_X_Series_1_4_0_Release_Notes.pdf), with TruPath Genome C2 or C8 flow cells. * Secondary analysis requires DRAGEN Germline v4.5 or later, in the cloud or via v4 DRAGEN Server. * Cloud analysis requires an active BaseSpace Sequence Hub or BioInsight Platform Core subscription. See [Software Registration](https://help.connected.illumina.com/account-management/rg-registration). {% endhint %}
## Pre-Sequencing and Set Up
Plan the run in BaseSpace Sequence Hub. Illumina TruPath Genome C2 and C8 Flow Cells are supported via the NovaSeq X Sequencing Systems. Sequencing must be performed on the [NovaSeq X Instrument Series](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html) using the [1.4 Software Package.](https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/novaseq-x-series/200079828_00_NovaSeq_X_Series_1_4_0_Release_Notes.pdf) Use run planning to set up DRAGEN Germline for cloud analysis, or for exporting a sample sheet for BCL Convert when converting on-premises. See [Instrument Sequencing & Run Setup](broken://spaces/EGUm4Hkqvb9yIqNHcUlp/pages/IrEkDI6NPYn2Z9o9hlA8) for prerequisites. ## DRAGEN Germline Secondary Analysis
DRAGEN Germline with Illumina TruPath Genome (also known as proximity mode) supports secondary analysis of TruPath data. TruPath Data may be analyzed on-premise via local DRAGEN server or in the cloud (BaseSpace Autolaunch or Platform Core). For more information on DRAGEN Secondary Analysis, please refer to the [DRAGEN User Guide.](https://help.connected.illumina.com/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-trupath-pipeline)\ \ Choose a deployment: * **Cloud** — A Bioinsight Platform Core account with a valid subscription is required for analyzing TruPath data in [Illumina Bioinsight Platform Core](https://www.illumina.com/products/by-type/informatics-products/connected-analytics.html). For analysis options and pipeline options, see the sections in [Cloud Analysis Settings.](/illumina-trupath-genome/run-analysis-setup/cloud-analysis-settings.md)
* **On Premises** — On-Prem DRAGEN Server Analysis, which requires a v4 DRAGEN Server. See the section on [On-Prem DRAGEN Server Analysis.](/illumina-trupath-genome/run-analysis-setup/on-prem-dragen-server-analysis.md) ## Data Visualization
TruPath data provides novel variant calling results which may be visualized using Illumina Bioinsight Platform Core's Genome Viewer functionality. Upon completion of DRAGEN TruPath Analysis, visualizations may be accessed on Platform Core. For more information on this, please visit the page [Visualize Data in Platform Core.](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-platform-core.md) DRAGEN Reports also offers novel visualizations for DRAGEN TruPath's Multi-Region Joint Detection (MRJD) calling, which provides haplotype resolved calls in paralogous regions. For more information, please visit the page [Visualize Data in DRAGEN Reports](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-dragen-reports.md). Third-party tools such as IGV and HiGlass are also compatible with DRAGEN TruPath Outputs. For more information, please visit the pages to[ Visualize Data in IGV](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-igv.md) and [HiGlass.](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-higlass.md) ## Interpretation Tertiary analysis and interpretation may be performed in Emedgene (EMG), with TruPath secondary analysis outputs ingestible by Emedgene. For more information, please [visit this link here.](https://help.emg.illumina.com/release-notes/workbench-and-pipeline-updates) ## Related Documentation This space covers the TruPath Genome software workflow. Assay, pipeline, and product references live elsewhere: | Topic | Reference | | ------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Library prep and assay workflow | [Illumina TruPath Genome Assay Guidance](https://support-docs.illumina.com/LP/TrupathGenome/Content/LP/FrontPages/TruPathGenome.htm) | | DRAGEN Germline pipeline & v4 DRAGEN Server | [DRAGEN User Guide](https://help.dragen.illumina.com/dragen-v4.6/product-guides/dragen-v4.6/dragen-trupath-pipeline) | | Sample and coverage recommendations | [TruPath Genome Data Sheet](https://support.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trupath-genome-data-sheet-m-gl-03931/trupath-genome-data-sheet-m-gl-03931.pdf), [TruPath Genome Tech Note](https://support.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trupath-genome-sample-info-tech-note-m-gl-03932/trupath-genome-sample-info-tech-note-m-gl-03932.pdf) | | Emedgene release notes | [Emedgene Workbench and Pipeline Updates](https://help.emg.illumina.com/release-notes/workbench-and-pipeline-updates) | | DRAGEN software installer (on-premises) | [TruPath Genome Software Downloads](https://support.illumina.com/downloads/trupath-genome-software.html) | | Product support | [Illumina TruPath Genome Support](https://support.illumina.com/sequencing/sequencing_kits/illumina-trupath-genome.html) | | MRJD App Note | [MRJD Application Note](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trupath-genome-app-note-m-gl-04321/trupath-genome-app-note-m-gl-04321.pdf) | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/illumina-trupath-genome/get-started/readme.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.