# Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6

The Illumina DRAGEN TruSight Oncology 500 (TSO 500) ctDNA Analysis Software supports analysis for DNA libraries that are isolated from plasma and prepared using TruSight Oncology 500 ctDNA v2 and v1 assays. The software, which can be run on the DRAGEN Server, on Illumina Connected Analytics, and as an analysis application on NovaSeq 6000Dx, produces a variant call file (VCF) for small variants. Other outputs include tumor mutational burden (TMB), a Jensen-Shannon divergence (sum JSD) score that can be used for evaluating microsatellite instability (MSI) status, files with copy number variants (CNV), fusions as well as coverage reports.

The secondary analysis software starts from a sequencing run folder containing base call files (BCL) or from FASTQ files staged in a FASTQ folder.

This document provides information on installation, configuration, running, troubleshooting as well as analysis algorithms of DRAGEN TruSight Oncology 500 ctDNA analysis software on Illumina Connected Analytics, standalone DRAGEN server, and the NovaSeq 6000Dx analysis application.

The software is optimized for analyzing sequencing outputs generated by the TruSight Oncology 500 ctDNA v2 and v1 assays. Modification might lead to inaccurate data and is a violation of the [Illumina Software Subscription Agreement](https://www.illumina.com/company/legal/terms-and-conditions.html).

{% hint style="info" %}
Variant reporting by DRAGEN TruSight™ Oncology 500 ctDNA Analysis Software is limited by a manifest file and a [block list file](/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/block-list.md). The manifest file excludes regions where the probe set does not effectively capture targets, and the block list file excludes specific positions from variant calling. TSO 500 ctDNA assay probes target at least 97% of the CDS of 474 genes. Please contact your local Illumina representative for more information if needed.
{% endhint %}

## Scope

This resource provides information on installation, configuration, running, troubleshooting and analysis algorithms for the following software:

<table><thead><tr><th width="619">Software</th><th>Versions</th></tr></thead><tbody><tr><td>DRAGEN TruSight Oncology 500 ctDNA Analysis Software on Illumina Connected Analytics (ICA)</td><td><ul><li>v2.6.0.25</li><li>v2.6.1.8</li><li>v2.6.3</li><li>v2.6.4</li></ul></td></tr><tr><td>DRAGEN TruSight Oncology 500 ctDNA Analysis Software (for standalone DRAGEN server)</td><td><ul><li>v2.6.0</li><li>v2.6.1</li><li>v2.6.2</li><li>v2.6.3</li><li>v2.6.4</li></ul></td></tr><tr><td>DRAGEN TruSight Oncology 500 ctDNA Analysis Application on NovaSeq 6000Dx (uses a paired DRAGEN server)</td><td><ul><li>v2.6.0</li><li>v2.6.1</li><li>v2.6.3</li></ul></td></tr></tbody></table>

The content is applicable to all software versions as listed for each deployment above, unless otherwise specified.

## Local and Cloud Deployments

Local analysis is available using a standalone DRAGEN server or an application with a user interface on NovaSeq 6000Dx. The software on the standalone DRAGEN server allows for analysis on a single DRAGEN server or splitting across multiple servers.

Cloud analysis is available on Illumina Connected Analytics with auto-launch or manual launch. Both methods are available from BCLs and FASTQs.

## Instrument Compatibility

DRAGEN TruSight Oncology 500 ctDNA analysis software is compatible with data generated on the Illumina instruments as summarized in the table below.

<table data-full-width="true"><thead><tr><th width="160">Instrument</th><th width="219">Illumina Connected Analytics</th><th>Standalone DRAGEN Server</th><th>Paired DRAGEN server</th><th>On-board DRAGEN</th></tr></thead><tbody><tr><td>NovaSeq 6000</td><td><mark style="color:green;">Yes</mark><br><mark style="color:green;">(v2.6.0.25, v2.6.1.8, v2.6.3)</mark></td><td><mark style="color:green;">Yes</mark></td><td>N/A</td><td>N/A</td></tr><tr><td>NovaSeq 6000Dx (RUO mode)</td><td><mark style="color:green;">Yes</mark><br><mark style="color:green;">(v2.6.0.25, v2.6.1.8, v2.6.3)</mark></td><td><mark style="color:green;">Yes</mark></td><td><mark style="color:green;">Yes</mark><br><mark style="color:green;">(v2.6.0, v2.6.1, v2.6.3)</mark></td><td>N/A</td></tr><tr><td>NovaSeq X</td><td><mark style="color:green;">Yes</mark><br><mark style="color:green;">(v2.6.0.25, v2.6.1.8, v2.6.3, v2.6.4)</mark></td><td><mark style="color:green;">Yes</mark></td><td>N/A</td><td><mark style="color:red;">No</mark></td></tr><tr><td>NextSeq2K</td><td><mark style="color:green;">Yes</mark><br><mark style="color:green;">(v2.6.3)</mark></td><td><mark style="color:green;">Yes</mark></td><td>N/A</td><td><mark style="color:red;">No</mark></td></tr></tbody></table>

## Navigation of Guide

This resource provides information on installation, configuration, running, troubleshooting as well as analysis algorithms of DRAGEN TruSight Oncology 500 ctDNA analysis software on Illumina Connected Analytics, standalone DRAGEN server, and the NovaSeq 6000Dx analysis application.

## Workflow Diagram

<figure><img src="/files/uMQDICxWMxxI35uXfsl0" alt=""><figcaption><p>Workflow Overview</p></figcaption></figure>


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