You can use the Run Planning tool in BaseSpace Sequence Hub to create and configure digitalMLPA run settings as described below.

1. In the BaseSpace sequence hub select the Runs tab.

2. Open the New Run dropdown menu.

3. Select Run Planning. The Create a Run wizard will open.

4. Enter a run name and optionally a run description, select your instrument platform and select the secondary analyis location.

   Please note that depending on the instrument used the fields appearing after this step might differ. For the MiSeq i100 and NovaSeq X series enter the information below in the Read Lengths field; for other instruments go to step 5.

   • Read 1 should be at least 110 nt.

   • Index 1, Index 2 and Read 2 should be "0".

5. Enter the Sample Container ID (optional).

6. Click Next, which will take you to the Configuration wizard.

7. Under Application, select the latest version of DRAGEN BCL Convert.

8. Optionally add a description.

9. Click on the Index Adapter Kit dropdown and select digitalMLPA if available. If you do not have this option yet (e.g. because this is your first run):

   • Choose Add Index Adapter Kit.

   • In the popup that appears, import this TSV file and click Create New Kit.

   • The digitalMLPA option should now be available.

10. Click on the Library Prep Kit dropdown and select digitalMLPA if available. If you do not have this option yet:

    • Click Add Custom Library Prep Kit.

    • In the popup that appears, enter this information:

      • Display Name: digitalMLPA.

      • Read Type: Single Read.

      • Default Read Cycle: 110.

      • Compatible Index Adapter Kits: digitalMLPA.

    • Click Create New Kit.

    • The digitalMLPA option should now be available.

11. Click Next. This will take you to the Configuration: DRAGEN BCL Convert page. Please note that the fields on this page differ per Illumina instrument.

12. Add a description.

13. Values for the library prep kit, index adapter kit, index read, read type, read lengths and override cycles should already be prefilled.

14. Enter the name of your sample. Please note that if you are using only digitalMLPA, i.e. not combining libraries, only one sample is inserted irrespective of the number of digitalMLPA reactions in your experiment.

15. If the field analysis settings appears, set FASTQ File Compression Format to gzip to minimize required hard drive space. If other fields are present, they can be left empty for a digitalMLPA-only run.

16. Click Next.

17. The run review will be shown where you can check if everything is correct before exporting the run sheet.

For questions about digitalMLPA, please contact us.