Using custom sequencing recipes on Illumina NovaSeq X Series instruments

Custom sequencing recipes are sometimes used for specific sequencing applications; these recipes introduce changes to the standard imaging and/or chemistry steps performed by the sequencer. Illumina does not guarantee performance for runs performed with third party custom recipes.

Run Setup using a custom recipes on Illumina NovaSeq X Series

1. Transfer the Custom Recipe files to the Downloads directory on the NovaSeq X Series instrument.

• Note: if using a USB device to transfer the custom recipe, for instruments running Control Software v1.3.1, see Knowledge Base article Validated USB Storage Devices for NovaSeq X Series Control Software v1.3.1 for approved USB external storage devices.

1. In the Files application, navigate to the Downloadsdirectory.

2. If the files are compressed, right-click on the compressed Custom Recipe files and select Extract Here...

   1. Note that the uncompressed Custom Recipe files extract to a sub-directory within Downloads. Navigate to this sub-directory within Downloads in Step 7.

3. Within the NovaSeq X Series Control Software, select the Start button, then select Sequencing, and choose the appropriate Side(s) to begin Run Setup.

4. Toggle to Manual setup, then confirm that Manual Run (generate BCLs Only) is selected.

5. Input Run Name and cycle number information.

6. Under the Review your run information UI, click Select... under Custom Recipe (Optional) and browse to the uncompressed Custom Recipe file within the Downloads directory, then click the blue Select button.

7. Select Load consumables and proceed with run setup.

For any feedback or questions regarding this article (Illumina Knowledge Article #10171), contact Illumina Technical Support [email protected].