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 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
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}
}