Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Project description
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
# clone repository
git clone git@github.com:maxibor/sam2lca.git
# work on the dev branch
git checkout dev
# work in the sam2lca conda environment
conda env create -f environment.yml
conda activate sam2lca
# install sam2lca in editable mode
pip install -e .
# Run the unit and integration tests
pytest -s -vv --script-launch-mode=subprocess
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
Project details
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