PEP compatible

PEPATAC is an ATAC-seq pipeline for ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches. It performs adapter trimming, mapping, peak calling, and creates bigwig tracks, TSS enrichment files, and other outputs.


PEPATAC produces quality control plots, summary statistics, and several data formats to set the stage for project-specific analysis.

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 convenient 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.