sam2lca

Lowest Common Ancestor from a SAM/BAM/CRAM sequence alignment file.

TLDR

Analysis of sequencing reads aligned to a DNA database with NCBI accession numbers, using the NCBI taxonomy

sam2lca analyze myfile.bam

See all options

sam2lca --help
sam2lca update-db --help
sam2lca list-db --help
sam2lca analyze --help

For further infos, check out the sam2lca documentation and tutorial

Installation

With Conda (recommended)

conda install -c conda-forge -c bioconda -c maxibor sam2lca

With pip

pip install sam2lca

For development purposes, from the dev branch

git clone git@github.com:maxibor/sam2lca.git
git checkout dev
conda env create -f environment.yml
conda activate sam2lca
pip install -e .

or

pip install git+ssh://git@github.com/maxibor/sam2lca.git@dev

Documentation

The documentation of sam2lca, including tutorials, is available here: sam2lca.readthedocs.io