Installation¶

Recommended: conda¶

The simplest way to install LongBarcodeQC is with conda. This pulls in the external tools (minimap2, samtools) and the compiled dependencies (parasail, cutadapt) automatically, on every supported platform — including Apple Silicon (osx-arm64) and ARM Linux, where parasail has no wheel on PyPI:

conda install -c conda-forge -c bioconda longbarcodeqc

Both channels are required: longbarcodeqc and the bioinformatics tools come from bioconda, while Python and the general-purpose libraries come from conda-forge.

Alternative: PyPI¶

LongBarcodeQC is also published on PyPI. Note that pip will not install minimap2 or samtools, and parasail has no prebuilt arm64 wheel, so install those dependencies with conda first:

conda install -c conda-forge -c bioconda minimap2 samtools parasail-python cutadapt
pip install LongBarcodeQC

Development version¶

pip install git+https://github.com/ArpiarSaundersLab/LongBarcodeQC.git

Verifying the installation¶

lbqc --version
lbqc --help