captnseq-toolkit

Analysis tools for CAPTn-seq (transposon-insertion sequencing) data. This package holds the scientific logic used by the nf-core/captnseq pipeline, so the pipeline itself only contains Nextflow code.

Install

pip install captnseq-toolkit        # once released on PyPI
conda install -c bioconda captnseq-toolkit   # once the Bioconda recipe is merged

Usage

captnseq-toolkit --help
captnseq-toolkit sam2sites    --help   # SAM -> insertion sites (BED + bedGraph)
captnseq-toolkit sites2genes  --help   # insertion sites -> per-gene counts
captnseq-toolkit essentiality --help   # per-gene counts -> essential / ambiguous / non-essential

Development

pip install -e ".[test]"
pytest

Releases are tagged vX.Y.Z (version comes from git tags via setuptools-scm).