Note:

• Use full paths when specifying the file paths in the command line.

• Avoid special characters such as &, *, #, and spaces.

• When starting from BCL files, only the run folder needs to be specified. The immediate parent directory containing the BCL files does not need to be specified.

When running the analysis software using SSH, Illumina recommends using additional software to prevent unexpected termination of analysis. Illumina recommends screen and tmux.

1. Wait for any running DRAGEN TruSight Oncology 500 ctDNA Analysis Software containers to complete before launching a new analysis. Run the following command to generate a list of running containers:docker ps

2. Select from one of the following options:

• Start from BCL files in the run folder with the sample sheet included in the run folder. DRAGEN_TSO500_CTDNA-2.6.0.sh \ --runFolder /staging/{RunFolderName} \ --analysisFolder /staging/{AnalysisFolderName}

• Start from BCL files in the run folder with the sample sheet located in a folder other than the run folder. DRAGEN_TSO500_CTDNA.sh \ --runFolder /staging/{RunFolderName} \ --analysisFolder /staging/{AnalysisFolderName} \

Starting from BCL Files

If starting from BCL (*.bcl) files, DRAGEN TruSight Oncology 500 ctDNA Analysis Software requires the run folder to contain certain files and folders. These inputs are required for Docker.

The run folder contains data from the sequencing run, make sure that the folder contains the following files:

Starting from FASTQ Files

The following inputs are required for running the DRAGEN TruSight Oncology 500 ctDNA Analysis Software using FASTQ (*.fastq) files. The requirements apply to Docker.

• Full path to an existing FASTQ folder.

• The FASTQ folder structure conforms to the folder structure in

• The sample sheet is in the FASTQ folder path, or you can set the path to the sample sheet with the --sampleSheet override command line option.

Make sure there is sufficient disk space for the analysis to complete. Refer to the --help command line argument details for disk space requirements.

FASTQ File Organization

Store FASTQ files in individual subfolders that correspond to a specific Sample_ID. Keep file pairs together in the same folder. Alternatively, store the FASTQ files in one flat folder structure where the FASTQ files are stored in one folder.

The DRAGEN TruSight Oncology 500 ctDNA Analysis Software requires separate FASTQ files per sample. Do not merge FASTQ files.

The instrument generates two FASTQ files per flow cell lane, so that there are eight FASTQ files per sample.

Sample1_S1_L001_R1_001.fastq.gz

• Sample1 represents the Sample ID.

• The S in S1 means sample, and the 1 in S1 is based on the order of samples in the sample sheet, so S1 is the first sample.

• L001 represents the flow cell lane number.

Methods for Launching Analysis

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.

Start the DRAGEN TruSight Oncology 500 ctDNA Analysis Software with the DRAGEN_TSO500_CTDNA-2.6.0.sh Bash script. The script is installed in the /usr/local/bin directory. The Bash script is executed on the command line and runs the software with Docker (or Apptainer if specified).

For arguments, refer to Command-Line Options. You can start from BCL files or from the FASTQ folder produced by BCL Convert. The following requirements apply for both methods:

• Path to the sequencing run or FASTQ folder. Copy the run or FASTQ folder to the DRAGEN server into the staging folder with the following recommended organization: /staging/runs/{RunID}. You can copy the run folder onto the DRAGEN server using Linux commands such as rsync. The sample sheet within the run folder is used unless otherwise specified through the command line.

• Run folder must be intact. Refer to for input requirements.

• If the analysis output folder path is different from the default, provide the analysis output folder path. Refer to .

Storage Requirements

For optimal performance, run analysis on data stored locally on the DRAGEN server. Analysis of data stored on NAS can take longer and performance can be less reliable.

The DRAGEN server provides an NVMe SSD in the /staging directory to use as the software output directory. Network-attached storage is required for long-term storage.

When running the DRAGEN TruSight Oncology 500 ctDNA Analysis Software, use the default settings or set the -analysisFolder command line option to a directory in /staging to make sure the DRAGEN server processes read and write data on the NVMe SSD.

Before beginning analysis, develop a strategy to copy data from the DRAGEN server to a network‑attached storage. Delete output data on the DRAGEN server as soon as possible.

The following are the run and analysis output sizes for each sequencing system per 101 bp:

When launching the analysis, the software checks that the minimum disk space required is available. If the minimum disk space is not available, the software shows an error message and prevents analysis from starting. If disk space is exhausted during a run, the run shows an error and stops analyzing.

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

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:

Input Validation Steps

In addition to sample sheet validation, before starting an analysis, the software performs the following checks:

• Resource bundle integrity

Auto-launch Prerequisites and Workflow

*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.

1. Use BaseSpace Sequence Hub Run Planning tool or the sample sheet templates provided on the support page to create and export a sample sheet.

   1. If BaseSpace Run Planning tool is not available in your region, use the sample sheet template.

2. Import the sample sheet to the instrument and start the sequencing run. Refer to for sample sheet guidance.

   1. Data is uploaded to BaseSpace Sequence Hub and then pushed to ICA. You can monitor the run in BaseSpace Sequence Hub.

   2. 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

3. View the analysis output results in either BaseSpace Sequence Hub or ICA.

BaseSpace Sequence Hub Requirements for ICA Auto-Launch

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.

Requeue Analysis

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.

Minimum Storage Requirements on ICA

Refer to the for information on how to manage accounts and subscriptions.

Guided Examples

Please review these guided examples of using DRAGEN TSO 500 Analysis Software with auto-launch 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.

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 .

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

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 . 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.

Known Limitations

• 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 .