Last 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
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
sam2lca-1.0.0b0.tar.gz
(26.9 kB
view hashes)
Built Distribution
sam2lca-1.0.0b0-py3-none-any.whl
(30.5 kB
view hashes)
Close
Hashes for sam2lca-1.0.0b0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0dbcd7c8142675012728599ed2d23d70aaffb004dc23c9bfa984150510f0ced6 |
|
MD5 | d1d230b6c2188c54e72dca9dd41d997a |
|
BLAKE2b-256 | bebb8df512ec087f69845118da33a8fd1748862f0c267e68cc0c7c2c9f213dc6 |