Damage parameter estimation for ancient DNA
Project description
PyDamage
Pydamage, is a Python software to automate the process of contig damage identification and estimation. After modelling the ancient DNA damage using the C to T transitions, Pydamage uses a likelihood ratio test to discriminate between truly ancient, and modern contigs originating from sample contamination.
Installation
With conda (recommended)
conda install -c bioconda pydamage
With pip
pip install pydamage
Install from source to use the development version
Using pip
pip install git+ssh://git@github.com/maxibor/pydamage.git@dev
By cloning in a dedicated conda environment
git clone git@github.com:maxibor/pydamage.git
cd pydamage
git checkout dev
conda env create -f environment.yml
conda activate pydamage
pip install -e .
Quick start
pydamage --outdir result_directory analyze aligned.bam
Note that if you specify
--outdir
, it has to be before the PyDamage subcommand, example:pydamage --outdir test filter pydamage_results.csv
CLI help
Command line interface help message
pydamage --help
Documentation
Cite
@article{Borry2021_pydamage,
author = {Borry, Maxime and Huebner, Alexander and Rohrlach, Adam B and Warinner, Christina G},
doi = {10.1101/2021.03.24.436838},
elocation-id = {2021.03.24.436838},
eprint = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838.full.pdf},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly},
url = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838},
year = {2021}
}
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