Installation

PyPIBiocondaDockerSource

pip install bsaseq

conda install -c bioconda bsaseq

docker pull arnstrm2/bsaseq
docker run --rm arnstrm2/bsaseq --help

git clone https://github.com/rcac-bioinformatics/bsaseq.git
cd bsaseq
pip install -e .

Requirements

• Python 3.9-3.13
• cyvcf2, numpy, pandas, scipy, matplotlib, click, rich (installed automatically)

The cyvcf2 dependency bundles htslib. On macOS, install htslib (brew install htslib) if a wheel is unavailable for your platform.

Optional: snpEff

Variant annotation (bsaseq run --annotate, bsaseq annotate) requires snpEff. The Docker image can bundle it:

docker build --build-arg INSTALL_SNPEFF=true -t bsaseq:snpeff .

Verify a local snpEff install with:

bsaseq check-snpeff

Verify

bsaseq --version
bsaseq --help