nvi-demux

nvi-demux is an operational demultiplexing and quality-control pipeline for Illumina MiSeq and NextSeq runs, developed for the Norwegian Veterinary Institute. It converts the data stored in /data/rawdata/ from BCL to FASTQ, runs FastQC and MultiQC and prepares structured output for upload to VIGASP (analysis) or NIRD (archiving). It runs under the seqtech user, but that is not a hard requirement.

Execution flow

systemd user timer -> demultiplex.py -> bcl2fastq -> FastQC -> MultiQC -> staging in /data/for_transfer/ -> upload to VIGASP or NIRD

Usage

The script runs every 20 minutes, on the dot, via a systemd user timer.

Run manually

Should you need to run it manually, log into seqtech as the seqtech user and run

/usr/local/bin/demultiplex.py <RunID1> <RunID2> ... <RunIDn>

is the Illumina run directory name under /data/rawdata/ you need to demultiplex.

Example:

/usr/local/bin/demultiplex.py 190912_M06578_0001_000000000-CNNTP

You can also run /usr/local/bin/demultiplex.py and it will discover all demultiplexed runs and run them in sequence one after the other.

See docs/ for architecture, deployment and QC metrics