When using BSSH Run Planning to generate a sample sheet to auto-Launch analysis on ICA, you must designate "Start from Fastq" to be True or False (default is False). If you choose "False", BSSH will kick off the TSO 500 pipeline normally using BCL input from the run folder.
If you choose "True" for this option, BSSH will run two ICA pipelines in sequence:
First, it will run the BCL Convert v3.10.9 pipeline to generate the FASTQ files
Second, it will kick off the TSO 500 ctDNA pipeline using the FASTQ files generated above as the input
Please note. Run QC metrics are generated inside the TSO 500 pipeline from interop files in the run folder. When starting TSO 500 ctDNA from FASTQ (via auto-launch or manual launch), Run QC metrics will not be generated.
When the auto-launched analysis completed, you will see the analysis result shows results from both the BCL Convert pipeline and the TSO 500 ctDNA pipeline, like below:
*The BaseSpace Sequence Hub setting for run monitoring and storage must be selected on the instrument to use DRAGEN TSO 500 ctDNA analysis auto-launch. For information on preparing your instrument for DRAGEN TSO 500 ctDNA Auto-launch, refer to the documentation for your instrument.
Use BaseSpace Sequence Hub Run Planning tool or the sample sheet templates provided on the support page to create and export a sample sheet.
If BaseSpace Run Planning tool is not available in your region, use the sample sheet template.
Import the sample sheet to the instrument and start the sequencing run. Refer to for sample sheet guidance.
Data is uploaded to BaseSpace Sequence Hub and then pushed to ICA. You can monitor the run in BaseSpace Sequence Hub.
Analysis auto launches in ICA when sequencing and the upload completes. You can monitor the status of the analysis in BaseSpace Sequence Hub or ICA
View the analysis output results in either BaseSpace Sequence Hub or ICA.
To avoid invalid sample sheet configurations, Illumina recommends using BaseSpace Run Planning tool to generate sample sheets. Using an invalid sample sheet can result in failed runs and analyses.
BaseSpace Run Planning tool is a multi-step workflow that generates a manual launch or auto-launch capable sample sheet for export and requires the following additional settings:
Access to BaseSpace Sequence Hub.
ICA Run Storage is enabled under BaseSpace Sequence Hub settings.
Refer to the for information on setting up a BaseSpace Sequence Hub project.
You can requeue analysis of a run via the run's Summary page in BaseSpace Sequence Hub.
Refer to the for more information on requeuing an analysis.
Refer to the for information on how to manage accounts and subscriptions.
Please review these guided examples of using DRAGEN TSO 500 Analysis Software with auto-launch on ICA:
NovaSeq X 25B
6000
NextSeq 2000 P4 Flow Cell
500
NovaSeq 6000/6000Dx (RUO) SP Flow Cell
500
NovaSeq 6000/6000Dx (RUO) S1 Flow Cell
1100
NovaSeq 6000/6000Dx (RUO) S2 Flow Cell
2500
NovaSeq 6000/6000Dx (RUO) S4 Flow Cell
4300
NovaSeq X 1.5B
2000
NovaSeq X 10B
4300
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 .
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 .
After adding the Bundle to the Project, an example dataset becomes available in the Demo_Data folder for the Project. 
 Upload the sequencing data: For information on viewing and uploading data, refer to the Data section in .
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 . When the required files are completed, start analysis.
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:
To launch an analysis via the ICA user interface, configure a DRAGEN TSO 500 ctDNA pipeline analysis with the following parameters.
FASTQ Folder Naming Requirements
When specifying input FASTQ folder names, avoid using folder names that consist entirely of numeric characters with a leading zero, as this will cause the software to error out.
Unsupported naming pattern:
For information about using pipelines, refer to .
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.
'01234' (numeric-only with leading zero)
Supported naming patterns:
'12340' (numeric without leading zero)
'sample01' (alphanumeric)
'A1234' (alphanumeric)
'test_sample' (alphanumeric with underscore)
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.
Illumina Connected Analytics (ICA) supports the following methods for launching DRAGEN TruSight Oncology 500 ctDNA Analysis Software.
Auto-launch—Stream run data directly from the instrument to ICA via a specially configured sample sheet and automatically begin DRAGEN TSO 500 ctDNA analysis.
—Initiate DRAGEN TSO 500 ctDNA analysis on ICA using the run files and sample sheet files in the project.
For more information about using ICA or BaseSpace Sequence Hub, refer to the following support pages on the Illumina support site.