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.

Run Setup for Local Mode from Sample Sheet Template

1. Download Sample Sheet v2 Template here.

2. Follow the guidance in the Sample Sheet v2 Resource NextSeq 1000/2000 Settings to complete the sample sheet.

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].