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[![Bioconda][bioconda-badge]][bioconda-link]
[![DOI][zenodo-badge]][zenodo-link]

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[language-badge]:       http://img.shields.io/badge/language-python-brightgreen.svg
[language-link]:        http://www.python.org/
[code-style-badge]:     https://img.shields.io/badge/code%20style-black-000000.svg
[code-style-link]:      https://black.readthedocs.io/en/stable/
[type-checking-badge]:  http://www.mypy-lang.org/static/mypy_badge.svg
[type-checking-link]:   http://mypy-lang.org/
[pep-8-badge]:          https://img.shields.io/badge/code%20style-pep8-brightgreen.svg
[pep-8-link]:           https://www.python.org/dev/peps/pep-0008/
[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/pybwa/branch/main/graph/badge.svg
[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybwa
[license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
[license-link]:         https://github.com/fulcrumgenomics/pybwa/blob/main/LICENSE
[python-package-badge]: https://github.com/fulcrumgenomics/pybwa/actions/workflows/tests.yml/badge.svg
[python-package-link]:  https://github.com/fulcrumgenomics/pybwa/actions/workflows/tests.yml
[pypi-badge]:           https://badge.fury.io/py/pybwa.svg
[pypi-link]:            https://pypi.python.org/pypi/pybwa
[pypi-downloads-badge]: https://img.shields.io/pypi/dm/pybwa
[pypi-downloads-link]:  https://pypi.python.org/pypi/pybwa
[bioconda-badge]:       https://img.shields.io/conda/dn/bioconda/pybwa.svg?label=Bioconda
[bioconda-link]:        http://bioconda.github.io/recipes/pybwa/README.html
[zenodo-badge]:         https://zenodo.org/badge/902029215.svg
[zenodo-link]:          https://doi.org/10.5281/zenodo.15029038
# pybwa

Python language bindings for [bwa][bwa-link].

<p>
<a href float="left"="https://fulcrumgenomics.com"><img src="logos/fulcrumgenomics.svg" alt="Fulcrum Genomics" height="100"/></a>
</p>

[Visit us at Fulcrum Genomics](https://www.fulcrumgenomics.com) to learn more about how we can power your Bioinformatics with pybwa and beyond.

<a href="mailto:contact@fulcrumgenomics.com?subject=[GitHub inquiry]"><img src="https://img.shields.io/badge/Email_us-brightgreen.svg?&style=for-the-badge&logo=gmail&logoColor=white"/></a>
<a href="https://www.fulcrumgenomics.com"><img src="https://img.shields.io/badge/Visit_Us-blue.svg?&style=for-the-badge&logo=wordpress&logoColor=white"/></a>

Install with `pip install pybwa` or `conda install -c bioconda pybwa`.

**Requires python 3.9+**

See documentation on [pybwa.readthedocs.org][rtd-link].

[rtd-link]: http://pybwa.readthedocs.org/en/stable
[bwa-link]: https://github.com/lh3/bwa
