How to setup a sequencing run for the NextSeq 1000/2000

There are four unique run modes on the NextSeq 1000/2000. See the guidance below on how to setup runs for each of these run modes.

See Knowledge Base article Run Mode Options for the NextSeq 1000/2000 for comparison of the run modes.

Using the v2 Sample Sheet Template for Local Mode Setup

1. To set up a run in Local Mode, refer to the "How to Use a Sample Sheet?" section in the Run Setup User Guide.

   1. You can download the v2 sample sheet template directly from the guide.

Run setup for Cloud Mode, Hybrid Mode, and Local Mode with sample sheet generated in BaseSpace Run Planning

1. Begin run setup workflow in BaseSpace Sequence Hub (BSSH) using the RUNS tab and select NEW RUN.

1. Then select RUN PLANNING.

1. Select NextSeq 1000/2000 from the Instrument Platform dropdown menu.

1. Enter the run information; Name, Analysis, etc.

1. Specify the type of analysis to be performed from the Application dropdown menu.

1. Select the Library Prep Kit and Index Adapter Kit from the dropdown menus.

1. Specify the run parameters.

Note: these values will automatically populate based on the Library Prep Kit and Index Adapter Kits selections, though the values can be changed.

1. Add samples and index information to sample list.

1. Specify the analysis options under Analysis Settings.

1. Review the run set up parameters and Save as Draft or Save as Planned. Note: Runs must be Saved as Planned to be viewed by the sequencer.

For any feedback or questions regarding this article (Illumina Knowledge Article #6688), contact Illumina Technical Support [email protected].