Planning a Manual Mode Run on NovaSeq X/X Plus

Background

There are two options to setup a Manual Mode run on the NovaSeq X/X Plus.

1. Manual Mode (Generate BCLs Only): Select this option if not performing secondary analysis (FASTQ Generation). Can import a sample sheet with samples names and indexes.

1. Import sample sheet for local analysis (Manual Mode) - Select this option to import a v2 sample sheet and perform secondary analysis.

Manual Mode Run Setup

1. To sign into the Control Software, enter the username and password, and then select Sign In.

2. Select Start.

3. Select an instrument side to perform the run.

4. At the top of the runs list, select Manual to switch to manual run entry.

5. If want to perform a local secondary analysis:

   1. For run type, select Import sample sheet for local analysis.

   2. Select and open the sample sheet v2 file. For information on sample sheet v2 formatting and requirements, refer to the Sample Sheet v2 Resource.

6. If do not want to perform a local secondary analysis for the manual run:

   1. For run type, select Manual run (generate BCLs only).

   2. Enter the Run Name (The run name can contain a maximum of 225 alphanumeric characters, spaces, dashes, and underscores).

   3. Select single or paired-end for the read type.

   4. Enter the number of cycles performed in each read:

   5. Read 1 — Enter the cycles number.

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

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

   8. Read 2 — Enter the cycles number.

   9. [Optional] Select the sample sheet. For information on sample sheet v2 formatting and requirements, refer to the Sample Sheet v2 Resource.

   10. Select Review to review the current run.

7. [Optional] If the instrument is connected to the cloud, is possible to select a cloud run setting.

8. Select the output folder.

9. [Optional] Select a custom recipe file, to download see NovaSeq X Plus Product Files

   1. Custom Recipes will be applied to the entire flow cell, for additional information see, How to use custom primers on the NovaSeq X/X Plus

   2. If using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit or the Illumina Stranded mRNA Prep kit, select the custom recipe required. See Custom recipes for Illumina Stranded libraries on NovaSeq X/X Plus

10. Proceed to Load Consumables and Start the run.

For Additional Information See, NovaSeq X Plus Product Documentation - Start a Manual Run

For any feedback or questions regarding this article (Illumina Knowledge Article #8540), contact Illumina Technical Support [e-mail].