# DRAGEN TSO 500 Guides

- [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)
- [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)
- [Contamination](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/contamination.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)
- [Quality Control](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/quality-control.md)
- [DNA Expanded Metrics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/quality-control/dna-expanded-metrics.md)
- [RNA Expanded Metrics](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/quality-control/rna-expanded-metrics.md)
- [Contamination](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/quality-control/contamination.md)
- [Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/troubleshooting.md)


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