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A modular, containerized pipeline for ATAC-seq data processing

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---

[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)

PEPATAC is a pipeline for ATAC-seq data. For more information see: http://pepatac.databio.org/

## Docs

Develop docs with:

```
mkdocs serve -f mkdocs.yml
```

Build and deploy with:

```
mkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/pepatac/
```

## Contributing

Pull requests welcome. Active development should occur in a development or feature branch.

## Contributors

* Jason Smith, jasonsmith@virginia.edu
* Nathan Sheffield, nathan@code.databio.org
* Jin Xu, jinxu9@stanford.edu
* Ryan Corces, rcorces@stanford.edu
* Vince Reuter, vreuter@protonmail.com
* Donald Campbell, https://github.com/donaldcampbelljr
* Others... (add your name)

## Citing

If you find PEPATAC useful in your research, please cite:

Jason P. Smith, M. Ryan Corces, Jin Xu, Vincent P. Reuter, Howard Y. Chang, and Nathan C. Sheffield. PEPATAC: An optimized ATAC-seq pipeline with serial alignments. bioRxiv (2021). <a href="https://doi.org/10.1101/2020.10.21.347054">DOI: 10.1101/2020.10.21.347054</a>

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