Command-Line Options

You can use the following command-line options with DRAGEN TruSight Oncology 500 Analysis Software. For examples, refer to .

To learn more about the input requirements, use the --help command-line option.

Option	Required	Description
--help	No	Displays a help screen with available options.
--analysisFolder	No	Path to the local analysis folder. The default location is /staging/DRAGEN_TSO500_Analysis_{timestamp}. If not using the default location, provide the full path to the local analysis folder. Folder must have sufficient space and must be on an NVMe SSD drive. For example, the /staging directory on the DRAGEN server. Refer to table in Installation Requirements for minimum disk space requirements.
--resourcesFolder	No	Path to the resource folder location. The default location is /staging/illumina/DRAGEN_TSO500/resources. If not using the default location, enter the full path to the resource folder.
--runFolder	Yes	Required when --fastqFolder is not specified. Provide the full path to the local run folder.
--fastqFolder	Yes	Required when --runFolder is not specified. Provide the full path to the local FASTQ folder. Analysis starts at this location.
--user	No	Optional for Docker. Specify the user ID to be used within the Docker container.
--version	No	Displays the version of the software.
--sampleSheet	No	Provide the full path, including file name, if not provided as SampleSheet.csv in the run folder.
--sampleOrPairIDs	No	Provide the comma-delimited sample or pair IDs that should be processed on this node with no spaces. For example, Pair_1,Pair_2,Sample_1.
--demultiplexOnly	No	Demultiplex to generate FASTQ only without additional analysis.
--gather	No	Follow this option for any directories with results that should be gathered into a single Results folder.
--hashtableFolder	No	Defaults to the DRAGEN hash table location created upon install. If not using the default location, enter the hash table location.

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.

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

docker ps

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.sh \

--runFolder /staging/{RunFolderName} \

--analysisFolder /staging/{AnalysisFolderName}

•

Start from BCL files in the run folder with a different sample sheet.

DRAGEN_TSO500.sh \

--runFolder /staging/{RunFolderName} \

--analysisFolder /staging/{AnalysisFolderName} \

--sampleSheet /staging/{SampleSheetName}.csv

•

Start from BCL files in the run folder with a different sample sheet and demultiplexing only.

DRAGEN_TSO500.sh \

--runFolder /staging/{RunFolderName} \

--analysisFolder /staging/{AnalysisFolderName} \

--sampleSheet /staging/{SampleSheetName}.csv \

--demultiplexOnly

•

Start from FASTQ with the sample sheet included in the FASTQ folder and with different resources and hash table folders.

DRAGEN_TSO500.sh \

--resourcesFolder /staging/illumina/DRAGEN_TSO500/resources \

--hashtableFolder /staging/illumina/DRAGEN_TSO500/ref_hashtable \

--fastqFolder /staging/{FastqFolderName} \

--analysisFolder /staging/{AnalysisFolderName}

•

Start from FASTQ folder with sample sheet included in the FASTQ folder and subset of samples or pairs.

DRAGEN_TSO500.sh \

--fastqFolder /staging/{FastqFolderName} \

--analysisFolder /staging/{AnalysisFolderName} \

--sampleOrPairIDs “Pair_1,Pair2”