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
• 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