Sample Sheet Generation

The sample sheet is generated on the step before the run, which is Dilute and Denature (NovaSeq 6000 v3.5) in the NovaSeq Standard protocol or Load to Flowcell (NovaSeq 6000 v3.5) in the NovaSeq Xp protocol. This step places samples on the library tube or flow cell that are loaded in the NovaSeq 6000 instrument.

In the default configuration, the Validate Run Setup and Generate Sample Sheet automation generates one CSV format sample sheet file for use with bcl2fastq v2.20 downstream analysis.

The sample sheet is uploaded to the NVCS via the /Illumina/Sequencer/v2/sequencing-run/files endpoint to the Sequencer API. The file endpoint allows for a file to be downloaded from the Clarity LIMS using OAuth (instead of Basic Authentication), which is required for the NovaSeq 6000 instrument.

The run recipe response sets the sample sheet URL to the link to download the file from this endpoint and sets the sampleSheetRequiresOAuth value to true.

The sample sheet content is controlled by the following master step fields that display in the Step Details area of the Record Details screen.

• Experiment Name
• Read 1 Cycles
• Read 2 Cycles
• Workflow
• Reverse Complement Workflow
• Samplesheet Format

Depending on Samplesheet Format field value selection, a v1 or v2 sample sheet is generated. For detailed information on the following items, refer to the Bcl2fastq2 Sample Sheet Generation section of Illumina Instrument Sample Sheets (NGS v5.17 and later):

• Sample sheet generation script parameters and usage
• Sample sheet data and configuration options
• Enabling unique FASTQ file names per sequencing run