pydamage 0.60

Damage parameter estimation for ancient DNA

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 conda-forge -c bioconda -c maxibor pydamage

With pip

pip install pydamage

Install from source to use the development version

Using pip

pip install git+ssh://[e-mail]/maxibor/pydamage.git@dev

By cloning in a dedicated conda environment

git clone [e-mail]: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

pydamage.readthedocs.io

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}
}