Damage parameter estimation for ancient DNA

Project description

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://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 aligned.bam reference.fa

CLI help

Command line interface help message

pydamage --help

Documentation

pydamage.readthedocs.io

Project details

Release history Release notifications | RSS feed

0.80

Sep 19, 2024

0.72

Sep 1, 2023

0.71

Aug 4, 2023

0.70

Mar 10, 2022

0.62

Jul 28, 2021

0.61

Jul 20, 2021

0.60

Jul 2, 2021

0.50b0 pre-release

Nov 18, 2020

This version

0.40

Sep 22, 2020

0.30

Jun 30, 2020

0.12 yanked

May 18, 2020

0.11 yanked

May 18, 2020

0.7

Mar 8, 2022

0.2

May 22, 2020

0.1 yanked

May 14, 2020

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