How to upload NovaSeq X/X Plus runs to ICA and to BaseSpace to enable run shares and transfers

Important notes:

• All NovaSeq X/X Plus will be uploaded to the backend storage for ICA (Illumina Connected Analytics), regardless of BaseSpace Sequence Hub (BSSH) account type and subscription status. This is true whether the run is uploaded from the instrument directly or using the BaseSpace CLI (command line interface) when using the NovaSeq X tag.

• Currently (as of BSSH 7.12) NovaSeq X/X Plus runs stored on ICA cannot be shared nor transferred to other users via BaseSpace.

• In order to upload to the backend storage for BaseSpace and thus allow sharing and transferring, the BaseSpace CLI can be used if the instrument type is set to NovaSeq 6000.

Uploading a run from the NovaSeq X/X Plus instrument to ICA (run data will be stored within ICA and visible on BSSH):

1. Open a terminal on the instrument and type screen then press Enter. (This will open a "screen" session which will continue running in the background, even if the terminal window is inadvertently closed.)

2. Type the command below in the terminal and modify it by replacing the content within the braces (the curly brackets {} ) including the braces themselves, with the name and folder for the run in question:

• bs upload run -t NovaSeqX -n {runName} --run-parameters=/usr/local/illumina/runs/{runFolder}/RunParameters.xml /usr/local/illumina/mnt/runs/{runFolder}  

3. Double check the command and if it looks correct, press Enter.

4. Once the upload is complete, type exit and press Enter to close the screen session. The terminal window can now be closed.

Uploading a run from the NovaSeq X/X Plus instrument to BaseSpace in enable run shares and transfers (run data will be stored within BSSH):

1. Open a terminal on the instrument and type screen and press Enter. (This will open a "screen" session which will continue running in the background, even if the terminal window is inadvertently closed.)

2. Type the command below in the terminal and modify it by replacing the content within the braces (the curly brackets {} ) including the braces themselves, with the name and folder for the run in question:

• bs upload run -t NovaSeq6000 -n {runName} --run-parameters=/usr/local/illumina/runs/{runFolder}/RunParameters.xml /usr/local/illumina/mnt/runs/{runFolder}  

• Note the change of instrument type to NovaSeq 6000 above.

3. Double check the command and if it looks correct, press Enter.

4. Once the upload is complete, type exit and press Enter to close the screen session. The terminal window can now be closed.

For additional information see How to requeue analysis on the NovaSeq X/X Plus.

For any feedback or questions regarding this article (Illumina Knowledge Article #7937), contact Illumina Technical Support [e-mail].