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 bioconda 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 --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
Cite
PyDamage has been published in PeerJ: 10.7717/peerj.11845
@article{borry_pydamage_2021,
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 = {https://peerj.com/articles/11845},
urldate = {2021-07-27},
volume = {9},
year = {2021}
}
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file pydamage-0.80.tar.gz
.
File metadata
- Download URL: pydamage-0.80.tar.gz
- Upload date:
- Size: 31.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.12.6
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0a21b707f1c07e5d898e271a5ac93534cad9841db1ed2a1945b074effc7b64f4 |
|
MD5 | ad81b2a0cb2d762243974462e121c553 |
|
BLAKE2b-256 | 58bf402cb9e19b64bd2d392f197ad546703426ddc5f5dede561c950963c8641e |
File details
Details for the file pydamage-0.80-py3-none-any.whl
.
File metadata
- Download URL: pydamage-0.80-py3-none-any.whl
- Upload date:
- Size: 36.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.12.6
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 02407e264afe759bea54bd8c54f0a5af0b686e9f3115d8e3e7c4b1ac86b5b9b2 |
|
MD5 | 998da31e35abfc7b81ab930a3c085209 |
|
BLAKE2b-256 | 8d4f99e5d2d098af0d35189269ad11225fe30d94c88cbcf99e6e3381585afddd |