Plan a NextSeq 1000/2000 Run

1. Select the Runs tab, and then select the New Run drop-down.

2. Select Run Planning.

3. Run Settings wizard will be loaded.

4. In the Run Name field, enter a unique name of your preference to identify the current run. The run name can contain a maximum of 255 alphanumeric characters, spaces, dashes, and underscores.

5. [Optional] In the Run Description field, enter a description of the current run. The run description can contain a maximum of 255 alphanumeric characters.

6. Select the Instrument Platform.

7. Select the analysis location. Depending on the selected instrument type, not all options may be available.

   • BaseSpace - Analyze sequencing data in the cloud.

   • Local - Analyze sequencing data on-instrument or generate a Sample Sheet v2 for Local or Hybrid mode.

8. [Optional] In the Library Tube ID field, optionally enter the library tube ID of the current run. The library tube id can contain a maximum of 255 alphanumeric characters.

9. Select Next

10. Configuration wizard will be loaded

11. Select an analysis type and version. For more information about secondary analyses, see DRAGEN Secondary Analysis Output Files on the system guide for your instrument or the BaseSpace Sequence Hub app documentation. If you selected DRAGEN Single Cell RNA analysis, see the NextSeq 1000/2000 Products Files page for information on third-party single cell RNA library prep kit compatibility.

    For on-instrument analysis, the version selected must match the version of DRAGEN installed on the instrument. To confirm the version of DRAGEN installed on the instrument, see DRAGEN Workflow and License Updates on the system guide for your instrument.

12. [Optional] Set up custom index kits as follows. If you are using more than one library, the libraries must have the same index read lengths.

    1. Select Add Custom Index Adapter Kit under the Index Adapter Kit dropdown.

    2. Select a template type and enter the kit name, adapter sequences, index strategies, and index sequences. Make sure the second index (i5) adapter sequences are in forward orientation.

    3. Select Create New Kit.

13. [Optional] Set up custom library prep kit as follows.

    1. Select Add Custom Library Prep Kit under the Library Prep Kit dropdown.

    2. Enter the name, read types, default read cycles, and compatible index adapter kits for your custom library prep kit.

    3. Select Create New Kit.

14. Select the following instrument settings. Depending on the library prep kit, recommended options are automatically selected. Some library prep kits have hard-coded number of indexes reads and read types, which cannot be changed.

    • Library prep kit

    • Index adapter kit

    • Number of index reads

    • Read type

    • Number of sequencing cycles per read

    If Not Specified is selected for library prep kit, enter the number of Index sequencing cycles to be used in the run.

15. Enter sample information into the Sample Data spreadsheet using one of the following options. To group samples for data aggregation during downstream analysis, assign a name for the group in the Project column.

    • Select Import Samples and the type of the import source file in the dropdown, either CSV or Sample Sheet, and then select your source file. If CSV file is selected, make sure that your file follows the template that can be downloaded by selecting Download Template button.

      If Sample Sheet is selected, make sure that your sample sheet meets the formatting requirements. If CSV is selected, make sure to use the correct template as the template can be different depending on the selected index adapter kit and index strategy. For more details, see Import Samples.

    • Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

      Fixed-layout index plates require entries for well position. Indexes that do not have a fixed layout require entries for i7 and i5 indexes. i5 indexes must be entered in the forward orientation.

    • Manually enter sample IDs and corresponding well positions or indexes. If Not Specified is selected for the library prep kit, enter Index 2 (i5) sequences in the forward orientation.