DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • F2 Support on ICA
  • DRAGEN TSO 500 Guides
    • DRAGEN TSO 500 v2.6
      • Introduction to DRAGEN TSO 500 Analysis Software v2.6.x
      • Getting Started
        • Installation of 2.6.0 on Standalone DRAGEN Server
        • Installation of 2.6.1 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • RNA Analysis Methods
        • Quality Control
        • Performance Testing
      • Troubleshooting
    • DRAGEN TSO 500 v2.5
      • Introduction to DRAGEN TSO 500 Analysis Software v2.5.x
      • Getting Started
        • Installation of 2.5.3 on Standalone DRAGEN Server
        • Installation of v2.5.4 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
          • Block List
        • Analysis Methods
          • FASTQ Generation
          • DNA Analysis Methods
          • RNA Analysis Methods
          • Quality Control
          • Performance Testing
      • Troubleshooting
  • DRAGEN TSO 500 ctDNA Guides
    • DRAGEN TSO 500 ctDNA v2.6
      • Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6
      • Getting Started
        • Installation of TSO 500 ctDNA v2.6.0 on Standalone DRAGEN Server
        • Installation of TSO 500 ctDNA v2.6.2 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 ctDNA Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
      • Analysis Output
        • DNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • Quality Control
      • Troubleshooting
  • Reference
    • Revision History
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  • Scope
  • Local and Cloud Deployments
  • Instrument Compatibility
  • Navigation of Guide
  • Workflow Diagram

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  1. DRAGEN TSO 500 ctDNA Guides
  2. DRAGEN TSO 500 ctDNA v2.6

Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6

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Last updated 5 months ago

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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 .

Scope

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

Software
Versions

DRAGEN TruSight Oncology 500 ctDNA Analysis Software on Illumina Connected Analytics (ICA)

  • v2.6.0

  • v2.6.1

DRAGEN TruSight Oncology 500 ctDNA Analysis Software (for standalone DRAGEN server)

  • v2.6.0

  • v2.6.1

  • v2.6.2

DRAGEN TruSight Oncology 500 ctDNA Analysis Application on NovaSeq 6000Dx (uses a paired DRAGEN server)

  • v2.6.0

The content is applicable to all 3 software versions unless otherwise specified. The content related to setting up and running the analysis on ICA is only relevant to software versions v2.6.0 and v2.6.1. The content related to the analysis application on NovaSeq 6000Dx is only relevant to v2.6.1.

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.

Instrument
Illumina Connected Analytics
Standalone DRAGEN Server
Paired DRAGEN server
On-board DRAGEN

NovaSeq 6000

Yes (v2.6.0 and v2.6.1)

Yes

N/A

N/A

NovaSeq 6000Dx (RUO mode)

Yes (v2.6.0 and v2.6.1)

Yes

Yes (v2.6.1)

N/A

NovaSeq X

Yes (v2.6.0 and v2.6.1)

Yes

N/A

No

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

Illumina Software Subscription Agreement
Workflow Overview