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PEP compatible

PEPATAC is a standardized ATAC-seq analysis pipeline designed to be modular and highly flexible. PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome (and more) serially, which improves alignment and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project.


PEPATAC includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. We have produced an interactive display of the output folder structure, which includes:

  • HTML report: an easily-navigable HTML report with pretty plots: HTML summary report demo.
  • Stats: an easily parsable stats file: Summary statistics demo file.
  • Signal tracks: bigWig signal tracks with options to produce: smoothed signal and exact (nucleotide-resolution); or nucleotide-resolution signal corrected for enzymatic sequence bias.
  • QC plots: fragment distributions, TSS enrichment scores, library complexities, FRiP, and more.
  • Processed data: project-level consensus peaks and peak count tables.

User interface

PEPATAC is a python script that runs on the command line (See usage). It can also read projects in PEP format. This means that PEPATAC projects are also compatible with other PEP tools, and output can be conveniently read into R using the pepr package or into Python using the peppy package. The pipeline itself is customizable, enabling a user to adjust individual command settings or even swap out specific software by editing a few lines of human readable configuration files.


You can download the latest version from the releases page, or find changes listed in the CHANGELOG.


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