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 conda (recommended)
conda install -c conda-forge -c bioconda -c maxibor pydamagepip install pydamageUsing pip
pip install git+ssh://git@github.com/maxibor/pydamage.gitBy cloning in a dedicated conda environment
git clone git@github.com:maxibor/pydamage.git
cd pydamage
conda env create -f environment.yml
conda activate pydamage$ pydamage --help
Usage: pydamage [OPTIONS] BAM
PyDamage: Damage parameter estimation for ancient DNA
Author: Maxime Borry
Contact: <borry[at]shh.mpg.de>
Homepage & Documentation: github.com/maxibor/pydamage
BAM: path to BAM/SAM/CRAM alignment file
Options:
--version Show the version and exit.
-w, --wlen INTEGER Window length for damage modeling [default: 35]
-p, --process INTEGER Number of processes [default: 2]
-m, --mini INTEGER Minimum reads aligned to consider reference
[default: 1000]
-c, --cov FLOAT Minimum coverage to consider reference [default:8]
-s, --show_al Show alignments representations
-pl, --plot Make the damage plots
--verbose Verbose mode
-o, --outdir PATH Output directory [default: pydamage_results]
--force Force overwriting of results directory
--help Show this message and exit.pydamage logic:
n_reads >=minimum reads OR coverage >= minimum coverage