Can NextSeq 1000/2000 run folders be set up to be deleted automatically?

No, there is no way to automatically delete local run folders on NextSeq 1000/2000. All file management tasks, including run folder deletion, must be performed through the Disk Management menu in the control software.

Illumina does not support using third party deletion tools, deleting files via Linux GUI (graphic user interface), or deleting files via CLI (command line interface) tools on the NextSeq 1000/2000. Deleting runs manually can negatively impact the control software.

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