PEP compatible

What is PEPATAC?

PEPATAC is an ATAC-seq pipeline. It trims adapters, maps reads, calls peaks, and creates bigwig tracks, TSS enrichment files, and other outputs. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches.

What makes PEPATAC better?

PEPATAC has many nice features, such as scalability, restartability, copious logging, portability, standardized reference genome assembly, nice QC plots, and beautiful HTML reports. But what really sets it apart from others are these key advantages:

  • Standard project organization: PEPATAC reads sample data formatted in standard PEP format. This means PEPATAC projects are compatible with other PEP tools, such as R analysis with pepr or Python using peppy.
  • Speed and memory use: PEPATAC is employs several speed optimizations, such as using GenomicDistributions. It requires substantially lower time and memory than other pipelines.
  • Prealignments: PEPATAC pioneers a prealignment strategy to filter mitochondrial reads, leading to faster runtime and more accurate alignment statistics.
  • Flexibility: Choose from multiple adapter trimmers, peak callers, and output options. Or, just use the defaults.


PEPATAC produces many outputs to set the stage for project-specific analysis:

Quick start

PEPATAC is a python script. Once you have all the prerequisites installed, you just run it on the command line (see usage for the complete arguments list): --input reads.fq.gz [options...]


The latest version is posted on GitHub releases, with changes in the CHANGELOG.