illumina DRAGEN TruSight Oncology 500 ctDNA Analysis Software on ICA User Guide
- June 3, 2024
- illumina
Table of Contents
illumina DRAGEN TruSight Oncology 500 ctDNA Analysis Software on ICA
ILLUMINA PROPRIETARY
Document # 200015532 v00
August 2022
For Research Use Only. Not for use in diagnostic procedures.
DRAGEN TruSight Oncology 500 ctDNA Analysis Software v1.2 on ICA User Guide
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This document and its contents are proprietary to Illumina, Inc. and its affiliates (“Illumina”), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.
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Document # 200015532 v00
For Research Use Only. Not for use in diagnostic procedures.
Getting Started
You can execute DRAGEN™ TruSight™ Oncology 500 (TSO 500) ctDNA Analysis
Software v1.2 on Illumina® Connected Analytics (ICA) v2.
Use the following instructions to configure an analysis run in the ICA
interface using graphical mode or command-line interface (CLI). For more
information about using ICA, refer to the Illumina Connected Analytics support
site page. For more information about running a TSO 500 analysis on ICA, refer
to the TruSight Oncology 500 ctDNA support site page.
Prerequisites
To use ICA to perform interactive data analysis, complete the following
prerequisites:
- Purchase ICA and enable ICA Flow.
- Upload sequencing data files to an ICA project.
- Make sure a TSO 500 bundle is available when setting up a project.
Analysis Modes and Configuration
In ICA v2, there are two modes available to launch analysis:
- Graphical user interface
- Command-line interface (CLI)
When starting a new analysis for DRAGEN TSO 500 ctDNA Analysis Software v1.2,
select a TSO 500 project, TSO 500 pipeline, and the appropriate storage size.
For DRAGEN TSO 500 ctDNA Analysis Software v1.2 on ICA v2, a small storage
size is typically not sufficient. Using the medium or large storage option is
recommended.
Graphical Mode
In graphical mode, the following pipeline run settings must be configured to
initiate a DRAGEN TSO 500 ctDNA Analysis Software v1.2 run successfully.
ICA CLI
The same configuration fields as described in Graphical Mode on page 1 must be
modified for each ICA CLI run.
Analysis Methods
The DRAGEN TSO 500 ctDNA Analysis Software v1.2 uses the following tools to
analyze sequencing data.
- Sample Sheet Validation
- Resource Verification
- Run QC
- FASTQ Generation
- FASTQ Validation
- Align Collapse Fusion Caller
- Stitched Realigned
- Copy Number Variant (CNV) Caller
- Microsatellite Instability (MSI) Scoring
- DNA Fusion Filtering
- Small Variant Calling
- Small Variant Filtering
- Phased Variant Calling
- Annotation
- Tumor Mutational Burden (TMB) Scoring
- Max Somatic VAF
- Variant Matching
- Merged Annotation
- Contamination
- DNA QC Metrics
- Sample Analysis Results
- Combined Variant Output
- Metrics Output
- Clean Up
For more information on analysis methods, refer to DRAGEN TruSight Oncology 500 ctDNA Analysis Software v1.2 User Guide (Document # 200017080).
Output Folders
This section describes each output folder generated during analysis and where
to find metric and analytic files when the pipeline is executed on ICA.
High-Level Folder Structure
Analysis Folder
The analysis folder contains the following two subfolders:
Results—Contains the aggregated MetricsOutput.tsvfile and the combined dsdm.jsonfile at the root level. Additionally, the Resultsfolder contains a subfolder for each sample.
Each sample subfolder contains files required for generating result metrics and the files relevant for analysis.
Logs_Intermediates —Contains folders for each task in the DRAGEN TSO 500 ctDNA Analysis Software v1.2 on ICA pipeline. The folders contain a copy of all the relevant files required to create the metric output files and report files. Each folder for a pipeline task contains combined log files at the root level and subfolders for each sample. The sample-specific files include log files, console output, error output, and any intermediate results.
If an analysis run is unsuccessful, the analysis folder reflects the state of the system at the time of analysis failure. For example, if the analysis run was unsuccessful, the Resultsfolder might not have been created and intermediate folders called Analysis_Node_1to Analysis_Node_6might be present.
Cromwell Executions
Cromwell log files are generated from the execution of the DRAGEN TSO 500
ctDNA Analysis Software v1.2 on ICA pipeline.
The files are grouped by the subworkflow and the pipeline task that is being
executed.
Revision History
Illumina
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techsupport@illumina.com
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For Research Use Only. Not for use in diagnostic procedures. © 2022 Illumina,
Inc. All rights reserved.
References
- Illumina | Sequencing and array solutions to fuel genomic discoveries
- Legal | Legal Information for this website
- TruSight Oncology 500 ctDNA Support
- Illumina Connected Analytics Support
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