How to plan a Local sequencing run on the NovaSeq X/X Plus

To plan a Cloud Sequencing Run, use the Run Planning tool in BaseSpace Sequence Hub. For additional information see: Plan a Cloud Sequencing Run

To plan a Manual Mode Run, refer to Planning a Manual Mode Run on NovaSeq X/X Plus knowledge article for more information.

1. Select the instrument icon at the bottom of the NovaSeq X Plus Control Software to open the global navigation menu.

1. Select Runs, then navigate to the Planned tab and select Create Run.

1. In Run Settings, enter the applicable options:

Run Name: A name to identify the current run (maximum of 255 alphanumeric characters, spaces, periods, dashes, and underscores are allowed).

Run Description: [Optional and cannot contain asterisks, brackets, or commas].

Read Lengths:

• Read 1 — Enter the cycles number.

• Index 1 — length of the index read for Index 1.

• Index 2 — length of the index read for Index 2.

• Read 2 — Enter the cycles number.

Library tube ID: [Optional and is on the label of your library tube strip].

Select Next.

1. In Configuration, enter:

Applications: Select the desired analysis applications

Description: [Optional]

Library Prep Kit: Select a kit

Index Adapter Kit: Select a kit

For information on adding custom library prep and index adapter kits, refer to Import Custom Library Prep and Index Adapter Kits.

Select Next.

1. Input the sample and indexes information (i5 indexes must be entered in the forward orientation).

Note: To import a sample sheet, select "Import Samples" option. Only v2 sample sheets can be imported. (Samples IDs can contain up to 100 alphanumeric characters, hyphens and underscores).

Select Next.

1. Review the run configuration.

Note: Up to 4 DRAGEN applications can be selected for on-board local analysis (1 BCL + 3 additional DRAGEN apps). To enable multiple DRAGEN analysis configurations per run, select "Add Another Configuration".

Note:One sample can be loaded in multiple lanes (Sample 5 in Lane 1 and 2), but you cannot include the same sample for two different App Configuration.

1. Select Save As Planned to complete the run details and plan for sequencing.

2. Select Sequencing in Control Software home screen.

1. Select the desired side.

1. Select the current planned run.

Note: To change account or sign in the BaseSpace account select Change account button

1. Select Review to check the run configuration and proceed loading the consumables and starting the run.

After sequencing, Secondary Analysis starts using local DRAGEN on instrument. For Additional Information See: Set Up Secondary Analysis

For Additional Information See: NovaSeq X Plus Product Documentation, Plan a Local Sequencing Run

For any feedback or questions regarding this article (Illumina Knowledge Article #8528), contact Illumina Technical Support [e-mail].