Last Commont Ancestor on SAM/BAM/CRAM alignment files
Project description
sam2lca
Lowest Common Ancestor from a SAM/BAM/CRAM sequence alignment file
Quick start
Quick analyis of sequencing reads aligned to a DNA database
sam2lca analyze myfile.bam
See all options
sam2lca --help
sam2lca update-db --help
sam2lca analyze --help
Installation
From source
git clone git@github.com:maxibor/sam2lca.git
conda env create -f environment.yml
conda activate sam2lca
pip install git+ssh://git@github.com/maxibor/sam2lca.git
From Conda
conda install -c conda-forge -c bioconda -c maxibor sam2lca
From Pypi
pip install sam2lca
Documentation
The documentation is available here: sam2lca.readthedocs.io
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