> 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/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/introduction-to-dragen-tso-500-analysis-software-v2.5.x.md).

# Introduction to DRAGEN TSO 500 Analysis Software v2.5.x

## Scope

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

* DRAGEN TruSight Oncology 500 Analysis Software on BioInsight Platform Core (formerly ICA) v2.5.2
* DRAGEN TruSight Oncology 500 Analysis Software v2.5.3 (for standalone DRAGEN server)
* DRAGEN TruSight Oncology 500 Analysis Software v2.5.4 (for standalone DRAGEN server)

The content is applicable to all 3 software versions unless otherwise specified. The content related to setting up and running the analysis on Platform Core is only relevant to v2.5.2.

## Overview

DRAGEN TruSight™ Oncology 500 Analysis Software supports data analysis for TruSight Oncology 500 Assay and TruSight Oncology 500 High-Throughput Assay, both Research Use Only (RUO).

The software provides local and cloud analysis for DNA and RNA libraries generated from formalin-fixed, paraffin-embedded (FFPE) tissue samples. The assays and the software are optimized to provide high sensitivity and specificity for low-frequency somatic variants across coding exons and additional regions of biological relevance in 523 genes for DNA biomarkers.

In addition, this software supports data analysis for TruSight Oncology 500 HRD (RUO), an optional add-on kit to TruSight Oncology 500, that enables detection of homologous recombination deficiency (HRD) through assessment of a genomic instability score (GIS).

{% hint style="info" %}
TruSight Oncology 500 HRD is not available in Japan
{% endhint %}

### DNA biomarkers:

* Single nucleotide variants (SNVs)
* Insertions
* Deletions
* Copy number variants (CNVs)
* Exon-level CNVs
* Multinucleotide variants (MNVs)
* Genomic Instability Score (GIS Score) \*

### DNA Immunotherapy Biomarkers:

* Tumor mutational burden (TMB)
* Microsatellite instability (MSI)

### RNA biomarkers (called from 55 genes):

* Fusions
* Splice variants

### Beta features:

* Absolute copy numbers (ACN)\*
* Loss of heterozygosity (LOH)\*
* Tumor fraction\*
* Ploidy\*

Details of the regions covered by the assays can be found in the assay manifest file. Contact your local Illumina representative for more information.

{% hint style="info" %}
\*Requires TruSight Oncology 500 HRD add-on kit
{% endhint %}

{% hint style="info" %}
Variant reporting by DRAGEN TruSight™ Oncology 500 Analysis Software is limited by a manifest file and a [block list file](/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods/dna-analysis-methods/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 assay probes target at least 97% of the CDS of 474 genes. Please contact your local Illumina representative for more information if needed.
{% endhint %}

## Local and Cloud Deployments

Local analysis is available using a standalone DRAGEN server. 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 Platform Core with auto-launch (from BCL) or manual launch (from BCLs and FASTQs), see exceptions for NextSeq 1000/2000 and NovaSeq X in the instrument compatibility tabel below.

## Instrument Compatibility

DRAGEN TruSight Oncology 500 analysis software v2.5.x is compatible with data generated on the Illumina instruments as summarized in the table below.

<table data-full-width="true"><thead><tr><th>Instrument</th><th>BioInsight Platform Core*</th><th>Standalone DRAGEN Server</th><th>Paired DRAGEN server</th><th>On-board DRAGEN</th></tr></thead><tbody><tr><td>NextSeq 550Dx (RUO mode)</td><td><mark style="color:green;">Yes</mark></td><td><mark style="color:green;">Yes</mark></td><td><mark style="color:red;">No</mark></td><td>N/A</td></tr><tr><td>NextSeq 500/550</td><td><mark style="color:green;">Yes</mark></td><td><mark style="color:green;">Yes</mark></td><td>N/A</td><td>N/A</td></tr><tr><td>NovaSeq 6000</td><td><mark style="color:green;">Yes</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></td><td><mark style="color:green;">Yes</mark></td><td><mark style="color:red;">No</mark></td><td>N/A</td></tr><tr><td>NextSeq 1000/2000</td><td><mark style="color:green;">Yes**</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>NovaSeq X</td><td><mark style="color:green;">Yes**</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>

\*Among v2.5.x, only DRAGEN TruSight Oncology 500 analysis software v2.5.2 is supported on Platform Core

\*\*For the data generated with NextSeq 1000/2000 and NovaSeq X, analysis can be started only from FASTQs (not from BCLs). Only manual launch is available for Platform Core.


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