Sample sheets for the NextSeq 1000/2000

The NextSeq 1000/2000 must use a v2 sample sheet to analyze run data with DRAGEN. For Local and Standalone runs with Proactive, Run Monitoring, and Storage run modes, the run must be started with a v2 sample sheet. If starting run from Cloud or Hybrid mode, a sample sheet is not required as sample information is provided from BaseSpace Instrument Run Setup.

• For Standalone mode with Proactive, Run Monitoring, and Storage, the control software does not use the v2 sample sheet for run setup information--it only requires the sample sheet to send to BaseSpace Sequence Hub for secondary analysis in DRAGEN.

v2 sample sheets can either be created in BaseSpace or by using the template provided on the support site.

• Cloud: BaseSpace > Run Planning > Local Mode > Export Sample Sheet.

• Sample Sheet v2 Resources: Template and Reference Guide NextSeq 1000 and 2000 Sequencing System Product Files.

After editing, use a portable or mounted network drive to transfer the sample sheet to the NextSeq 1000 and NextSeq 2000 Sequencing Systems. The sample sheet can be placed on the NextSeq 1000/2000 instrument or remain on the portable/mounted drive. When the sample sheet is selected in the control software, it is copied to a pre-run folder on the instrument so the portable drive can be removed.

v1 sample sheets generated by Illumina Experiment Manager (IEM) are incompatible with DRAGEN analysis workflows. If running in Standalone mode with Proactive, Run Monitoring and Storage NextSeq 1000/2000 control software will not provide a warning when starting a run with a v1 sample sheet, but data will not analyze properly in DRAGEN BaseSpace applications.

For any feedback or questions regarding this article (Illumina Knowledge Article #3315), contact Illumina Technical Support [e-mail].