Pydamage, is a Python software to automate the process of contig damage identification and estimation. It uses a process akin to a likelihood ratio test to attempt to discriminate between truly ancient, and modern contigs originating from sample contamination.


Pydamage is not yet on pypi nor conda, but you can already install it using pip, provided that you have access to this repository.

Install dependencies in conda environment

git clone
cd pydamage
conda env create -f environment.yml
conda activate pydamage

Install pydamage

  • from source
python install
  • from Github using pip
pip install git+ssh://

CLI help

Command line interface help message

pydamage --help

See also CLI