A Python package and executable for Linux to help manage Illumina sequencing runs.

Umbra will watch a directory for incoming sequencing runs and dispatch a number of parallel processors to handle new run data. Automated processing tasks include adapter trimming, read interleaving, basic contig assembly, uploading finished datasets to Box, and alerting end users via email. A CSV report is refreshed on disk that summarizes processing status. A readonly mode allows for watching/reporting without processing.

An illumina sub-package provides some basic parsers for various Illumina file and directory fomats that can be used independently of the automated processing functionality.

Requirements:

• Python 3.7+ with packages: Biopython, BoxSDK, PyYAML, cutadapt
• Other programs: SPAdes, PEAR
• Box API credentials for automated uploads (optional)
• Access to an SMTP mail server for sending mail, for example, a local postfix installation (optional)

Limitations/assumptions:

• Tested with MiniSeq and MiSeq output
• Assumes the GenerateFASTQ workflow is enabled on the sequencer