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.


With pip

pip install pydamage

Install from source to use the development version

Using pip

pip install git+ssh://

By cloning in a dedicated conda environment

git clone
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



PyDamage has been published in PeerJ: 10.7717/peerj.11845

    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 = {},
    urldate = {2021-07-27},
    volume = {9},
    year = {2021}