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 processes (run folder deletion) must be processed through the Disk Management menu. Illumina strongly discourages 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.

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