Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA

How to Launch Analysis

1. Create a Project: Project can be specific for the DRAGEN TruSight Oncology 500 ctDNA pipeline or it can contain multiple Pipelines and/or Tools). For information on creating Projects, refer to the Projects section in Illumina Connected Analytics help.

ICA standard storage is used by default as soon as the Project is saved. To connect a different storage source, set it up before creating your Project. For details and options, refer to the Storage section in Illumina Connected Analytics help.

1. Edit Project and Add Bundle: Edit the Project and add the bundle titled, "DRAGEN TSO 500 ctDNA v2.6.0 (XX)." XX is a 2-letter code designating the region from which you are launching the analysis. Adding the Bundle automatically adds the pipeline and associated resource files and datasets to the Project. For information on Bundles, refer to the Bundles section in Illumina Connected Analytics help.

After adding the Bundle to the Project, an example dataset becomes available in the Demo_Data folder for the Project. 

1.  Upload the sequencing data: For information on viewing and uploading data, refer to the Data section in Illumina Connected Analytics help.

2. Start Analysis: In the Project, navigate to Pipelines, select the TSO 500 ctDNA v2.6.0 Pipeline, and then select  "Start New Analysis". Set up the new analysis by configuring the parameters listed in the table below. When the required files are completed, start analysis.

3. Download Results: After analysis is complete, navigate to results in the configured output location.

Please see the Illumina Support Shorts for guidance on how to set up and run DRAGEN TSO 500 RUO analysis on ICA. This is the same process as DRAGEN TSO 500 ctDNA, but with different inputs specific to DRAGEN TSO 500 solid:

Analysis Parameters on ICA

To launch an analysis via the ICA user interface, configure a DRAGEN TSO 500 ctDNA pipeline analysis with the following parameters.

Parameter Name	Description
User Reference	The analysis run name.
User Tags	Text labels to help index the analysis.
Notify me when task is completed	Option to receive an email notification when analysis is complete.
Output Folder	The path to the analysis output folder. The default path is the project output folder.
Entitlement Bundle	Automatically populated from the project details.
Sample Sheet	Select a sample sheet in CSV format for the analysis. To note: Sample Sheet selection is optional if starting from a run folder, and required when submitting a FASTQ folder.
Input Folder	The run folder or FASTQ folder that contains files to analyze.
FASTQ List CSV	Do not use, this only applies to auto-launch TSO 500 ctDNA analysis from FASTQs after BCL auto-launch.
Starts from FASTQ	True for analysis performed on files in the FASTQ folder. False for analysis performed on files in the run folder.
Sample or Pair IDs	Optional subset of Sample IDs or Pair IDs to analyze.
Sample List	Do not use, this only applies to auto-launch TSO 500 ctDNA analysis from FASTQs after BCL auto-launch.
Storage Size	The storage size to allocate for the analysis. The default and recommended value is Large.

For information about using pipelines, refer to Illumina Connected Analytics support site page.