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 bioconda 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

Cite

sam2lca has been published in JOSS with the following DOI: 10.21105/joss.04360

@article{Borry2022,
  doi = {10.21105/joss.04360},
  url = {https://doi.org/10.21105/joss.04360},
  year = {2022},
  publisher = {The Open Journal},
  volume = {7},
  number = {74},
  pages = {4360},
  author = {Maxime Borry and Alexander Hübner and Christina Warinner},
  title = {sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files},
  journal = {Journal of Open Source Software}
}