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 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}
}
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