fcid

flow cell ID: parse illumina fastq headers to determine machine and flowcell type Thanks to:

• https://www.biostars.org/p/198143/
• https://github.com/10XGenomics/supernova/blob/master/tenkit/lib/python/tenkit/illumina_instrument.py#L12-L45
• Illumina Techinical Support

Disclaimer: this is not a replacement for proper sequencing run tracking. Disclaimer: PRs welcome to fill gaps! Instrument IDs are less reliable as those are often changed by the sequencing center.

Got ONT data? Their flowcells do not follow a naming convention, but they can look up flowcells internally; contact them via the support page on their website.

Installation

pip install fcid
# or, for you devs
git clone <this repo> && cd fcid
pip install --editable .

Usage (CLI)

# fcid CABBCANXX
# fcid  K11111 --by-machine
# fcid 22C37GLT3

Usage (package)

>>> from fcid import run
>>> run.get_tech_type("CABBCANXX", run.FCIDs)
[['HiSeq 2500'], 'High Output v3 flow cell']

Test

pytest -s # see detailed logs by

Deployment

1. Update version pyproject.toml
2. commit and tag
3. push to github and make a release
4. check the package deployment action