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alt=\"PyDamage\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://github.com/maxibor/pydamage/releases\"\u003e\u003cimg src=\"https://img.shields.io/github/v/release/maxibor/pydamage?include_prereleases\u0026label=version\"/\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/maxibor/pydamage/actions\"\u003e\u003cimg src=\"https://github.com/maxibor/pydamage/workflows/pydamage_ci/badge.svg\"/\u003e\u003c/a\u003e\n    \u003ca href=\"https://pydamage.readthedocs.io\"\u003e\u003cimg src=\"https://readthedocs.org/projects/pydamage/badge/?version=latest\"/\u003e\u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/pydamage/\"\u003e\u003cimg src=\"https://img.shields.io/badge/install%20with-pip-blue\"/\u003e\u003c/a\u003e\n    \u003ca href=\"https://anaconda.org/bioconda/pydamage\"\u003e\u003cimg src=\"https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat\"/\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n# PyDamage\n\nPydamage, is a Python software to automate the process of contig damage identification and estimation.\nAfter 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.\n\n## Installation\n\n### With [conda](https://docs.conda.io/en/latest/) (recommended)\n\n```bash\nconda install -c bioconda pydamage\n```\n\n### With pip\n\n```bash\npip install pydamage\n```\n\n### Install from source to use the development version\n\nUsing pip\n\n```bash\npip install git+ssh://git@github.com/maxibor/pydamage.git@dev\n```\n\nBy cloning in a dedicated conda environment\n\n```bash\ngit clone git@github.com:maxibor/pydamage.git\ncd pydamage\ngit checkout dev\nconda env create -f environment.yml\nconda activate pydamage\npip install -e .\n```\n\nRunning tests\n\n```bash\npython -m pytest\n```\n\n\n## Quick start\n\n```bash\npydamage --outdir result_directory analyze aligned.bam\n```\n\n\u003e Note that if you specify `--outdir`, it has to be before the PyDamage subcommand, example: `pydamage --outdir test filter pydamage_results.csv`\n\n## CLI help\n\nCommand line interface help message\n\n```bash\npydamage --help\n```\n\n## Documentation\n\n[pydamage.readthedocs.io](https://pydamage.readthedocs.io)\n\n## Cite\n\nPyDamage has been published in PeerJ: [10.7717/peerj.11845](https://doi.org/10.7717/peerj.11845)\n\n```\n@article{borry_pydamage_2021,\n    author = {Borry, Maxime and Hübner, Alexander and Rohrlach, Adam B. and Warinner, Christina},\n    doi = {10.7717/peerj.11845},\n    issn = {2167-8359},\n    journal = {PeerJ},\n    language = {en},\n    month = {July},\n    note = {Publisher: PeerJ Inc.},\n    pages = {e11845},\n    shorttitle = {PyDamage},\n    title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly},\n    url = {https://peerj.com/articles/11845},\n    urldate = {2021-07-27},\n    volume = {9},\n    year = {2021}\n}\n\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fpydamage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxibor%2Fpydamage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fpydamage/lists"}