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
PyDamage has been published in PeerJ: 10.7717/peerj.11845
@article{borry_pydamage_2021,
author = {Borry, Maxime and Hübner, Alexander and Rohrlach, Adam B. and Warinner, Christina},
doi = {10.7717/peerj.11845},
issn = {2167-8359},
journal = {PeerJ},
language = {en},
month = {July},
note = {Publisher: PeerJ Inc.},
pages = {e11845},
shorttitle = {PyDamage},
title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly},
url = {https://peerj.com/articles/11845},
urldate = {2021-07-27},
volume = {9},
year = {2021}
}