Create a Project: Project can be specific for the DRAGEN TruSight Oncology 500 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 v2.5.2 (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, desired TSO 500  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.
To launch an analysis via the ICA user interface, configure a DRAGEN TSO 500 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.
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.
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.
*The BaseSpace Sequence Hub setting for run monitoring and storage must be selected on the instrument to use DRAGEN TSO 500 analysis auto-launch. For information on preparing your instrument for DRAGEN TSO 500 Auto-launch, refer to the documentation for your instrument.
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 ICA Auto-launch Sample Sheet Requirements 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
If necessary, you can requeue the analysis via BaseSpace Sequence Hub.
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.
For the data generated by NextSeq 1000/2000 and NextSeq X, only manual option for launching analysis on ICA is available. The analysis can only start from FASTQs files.
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 BaseSpace Sequence Hub support site page 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 BaseSpace Sequence Hub support site page for more information on requeuing an analysis.
NextSeq 500/550/550Dx (RUO) HO flow cell
350
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
Refer to the Software Registration page 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 10B
4300
NovaSeq X 25B
8400
NextSeq 1000/2000
350
Illumina Connected Analytics (ICA) supports the following methods for launching DRAGEN TruSight Oncology 500 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 analysis.
—Initiate DRAGEN TSO 500 analysis on ICA using the run files and sample sheet files in the project.
For the data generated by NextSeq 1000/2000 and NextSeq X, only manual option for launching analysis on ICA is available. The analysis can only start from FASTQs files.
For more information about using ICA or BaseSpace Sequence Hub, refer to the following support pages on the Illumina support site.