How to plan a Local sequencing run on the NovaSeq X Series

Background

The NovaSeq X allows users to setup sequencing runs using Local or Cloud Run Planning, importing a Sample Sheet, or Manual mode. See the following steps to setup a sequencing run using Local Run Planning options.

For more information on Run Modes, see Knowledge Article Run Mode options for the NovaSeq X Series

To setup a Manual Mode Run, refer to Knowledge Article Planning a Manual Mode Run on NovaSeq X Series for more information.

Using Local Run Planning

1. Select the instrument icon at the bottom of the NovaSeq X Series 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].

Generate FastQC metrics: If enabled, the analysis pipeline generates FastQC metrics.

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.

All Read Length fields must have a numerical value input. To skip a Read, input 0 for the number of cycles for that Read.

Note for NovaSeq X Control Software v1.3 and above: Library tube ID is renamed as Sample Container ID.[Optional and is on the label of the 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).

To import samples, select Download template and fill out the Sample ID and Index information, then select Import Samples and import the filled out template file.

Select Next.

1. Review the run configuration.

Note for NovaSeq X Control Software 1.2.2 and below: Up to 4 DRAGEN applications can be selected for on-board local analysis (1 BCL + 3 additional DRAGEN apps). Up to 8 DRAGEN applications can be selected for cloud analysis (1 BCL + 7 additional DRAGEN apps). Enter up to 8 Library Prep and Index Adapter kits combinations, per App (DRAGEN App + genome) configuration.

To enable multiple DRAGEN analysis configurations per run, select "Add Another Configuration".

Note for NovaSeq X Control Software 1.3 and above: Up to 12 DRAGEN applications plus 1 BCL Convert application can be selected for both on-board and cloud analysis. Enter up to 32 Library Prep and Index Adapter kits combinations, per App (DRAGEN App + genome) configuration.

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. In the global navigation menu, select Start and then Sequencing in Control Software home screen.

3. 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.

Using custom sequencing primer:

NovaSeq X Control Software v1.2.2 and below: Select the appropriate custom primer recipe XML file.

NovaSeq X Control Software v1.3 and above: Select the applicable custom primer checkboxes. Uploading a custom recipe disables the custom primer checkboxes.

For more information on custom primers, refer to Custom Primers.

Confirm the output folder before proceeding. For information on selecting the applicable Output folder, see article How to configure External Storage locations on the NovaSeq X/X Plus

1. Load the consumables and start the run.

After sequencing, Secondary Analysis starts with 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].