# DRAGEN TSO 500 ctDNA v2.6

- [Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6](https://help.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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 on Standalone DRAGEN Server](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/getting-started/installation-of-tso-500-ctdna-v2.6.2-v2.6.3-on-standalone-dragen-server.md)
- [Getting Started on Illumina Connected Analytics](https://help.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning.md)
- [Sample Sheet Introduction](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/run-planning/sample-sheet-introduction.md)
- [Sample Sheet Requirements](https://help.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/launching-analysis.md)
- [Analysis Launch on Standalone DRAGEN Server](https://help.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/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.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output.md)
- [Combined Variant Output](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/combined-variant-output.md)
- [Metrics Output](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/metrics-output.md)
- [DNA Expanded Metrics](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/metrics-output/dna-expanded-metrics.md)
- [Coverage Reports](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/coverage-reports.md)
- [Block List](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/block-list.md)
- [Analysis Methods](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods.md)
- [FastQ Generation](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fastq-generation.md)
- [Mapping and Alignment](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/mapping-and-alignment.md)
- [Quality Control](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/quality-control.md)
- [Run QC](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/quality-control/run-qc.md)
- [Sample QC](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/quality-control/sample-qc.md)
- [Contamination](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/quality-control/contamination.md)
- [Small Variants](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/small-variants.md)
- [Fusions](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fusions.md)
- [CNV](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/cnv.md)
- [TMB](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/tmb.md)
- [MSI](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/msi.md)
- [Maximum Somatic VAF](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/max-somatic-vaf.md)
- [Troubleshooting](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/troubleshooting.md)