Starting From FASTQ Files

The following inputs are required for running the DRAGEN TruSight Oncology 500 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 FASTQ File Organization.
• The sample sheet is in the FASTQ folder path, or you can set the path to the sample sheet with the --sampleSheet override command.

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

BCL Convert has been set to write UMI sequences to the read headers in the FASTQ files.

Store FASTQ files in individual subfolders that correspond to a specific Sample_ID. Keep file pairs together in the same folder.

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

Folder structure must match exactly and cannot have extra or missing files. Analysis fails if FASTQ input files are structured incorrectly.

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.
• The R in R1 means Read, so R1 refers to Read 1.