How to requeue analysis on the NovaSeq X/X Plus

The NovaSeq X/X Plus can perform data analysis using the on-board DRAGEN server built into the platform. This guide discusses different ways to requeue analyses using the integrated Illumina Run Manager interface within the NovaSeq X Series Control Software.

Analysis of a NovaSeq X/X Plus run in BaseSpace Sequence Hub requires a correctly formatted v2 sample sheet. Illumina strongly recommends using the BaseSpace Run Planning tool to generate a sample sheet for analysis to ensure the required fields are correct.

The requeue analysis option will not be available through the Control Software if:

• A sequencing run or maintenance wash is in progress on the instrument.

• The run data was deleted from the instrument.

How to perform local analysis of Manual or Cloud Runs

Use the steps below to setup a new analysis from a Manual or Cloud run using run data stored on the NovaSeq X/X Plus instrument.

1. From the Control Software home screen, select the instrument icon to open the global navigation menu, then select Runs.

2. In the Runs window, select the Completed tab.

3. Select the run of interest listed under the Run Name column to open the Run Details page.

4. Under the Secondary analysis header, select Requeue Analysis.

5. In the popup window, select Requeue analysis from sample sheet.

6. Select the Upload button, then navigate to the v2 sample sheet file.

7. Enter the file path to the intended Output Folder on the External Storage.

8. Enter a description for the requeue in the Reanalysis Reason field.

9. Select Requeue Analysis when finished.

How to requeue analysis of a Local run

Use the steps below to requeue analysis of data from a Local run on the NovaSeq X/X Plus. This workflow is useful when editing sample index combinations or to add/remove DRAGEN Applications from the analysis workflow.

1. From the Control Software home screen, select the instrument icon to open the global navigation menu, then select Runs.

2. In the Runs window, select the Completed tab.

3. Select the run of interest listed under the Run Name column to open the Run Details page.

4. Under the Secondary analysis header, select Requeue Analysis.

5. In the popup window, select one of the following options.

   1. Requeue analysis from this run - Configure analysis using the Illumina Run Manager user interface.

   2. Requeue analysis from sample sheet - Configure analysis settings using a v2 sample sheet.

      1. Select the Upload button to select a v2 Sample sheet.

6. Enter the file path to the intended Output Folder on the External Storage.

7. Enter a description for the requeue in the Reanalysis Reason field.

8. Select Requeue Analysis when finished.

9. When selecting the Requeue analysis from this run option, perform any of the following actions as necessary:

   1. To include additional configurations, select Add configuration.

   2. To exclude a configuration from the requeue, select Delete next to the configuration name.

   3. To change configuration information, select Edit next to the configuration name.

10. Select Requeue Analysis when finished.

How to requeue analysis performed on BaseSpace Sequence Hub

• Analysis of a NovaSeq X/X Plus run in BaseSpace Sequence Hub requires a correctly formatted v2 sample sheet. Using BaseSpace Run Planning is strongly recommended to generate a sample sheet for reanalysis to ensure the required fields are correct.

• To requeue a NovaSeq X/X Plus run on BaseSpace, user can requeue through Run Summary page in BaseSpace or use BCL Convert App on BaseSpace.

Requeue a Cloud NovaSeqX/X Plus run through Run Summary Page

1. From the BaseSpace Sequence Hub home page, select Runs at the top of the page, then select the sequencing run from the list of completed sequencing runs.

2. From the Summary page, select Status option, then Requeue, then Planned Run

3. Click the radio button to select the Sample Sheet source to be opened in the Run Planning tool and select Continue.

1. If using a new Sample Sheet, the new sample sheet can be uploaded to BaseSpace.  

4. If needed, edit the analysis configuration after importing Sample Sheet then select Requeue to start the new analysis.

Requeue NovaSeq X/X Plus run with the BCL Convert app

1. From the BaseSpace Sequence Hub Home page, select Projects at the top of the page.

   1. To requeue an analysis within an existing Project, select the appropriate Project from the list.

   2. To create a new Project, select the File icon, then select New and follow the prompts to create a new Project.

2. Upload the corrected sample sheet to a project by selecting the File icon, then selecting Upload,then Files. Select the Misc/Other file type and import the v2 sample sheet CSV file.

3. Navigate to the BCL Convert appand select Launch Application from the app page.

4. Click on Select Runs to choose a run uploaded to your BaseSpace Sequence Hub account.

5. Under Override Sample Sheet, click Select Dataset File(s) to select the sample sheet uploaded in Step 2.

   1. Launching the BCL Convert app without a new sample sheet will use the previous sample sheet already in the run folder.

6. Select Launch Application to start the new analysis.

For any feedback or questions regarding this article (Illumina Knowledge Article #7765), contact Illumina Technical Support [e-mail].