kee007ney / pepatac

A modular, containerized pipeline for ATAC-seq data processing

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PEPATAC is a pipeline designed to process 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, [e-mail]
• Nathan Sheffield, [e-mail]
• Jin Xu, [e-mail]
• Ryan Corces, [e-mail]
• Vince Reuter, [e-mail]
• 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). DOI: 10.1101/2020.10.21.347054