PEP compatible

PEPPRO is a pipeline designed to process PRO-seq data. It is optimized on unique features of PRO-seq to be fast and accurate. It performs adapter removal, including UMI of variable length, read deduplication, trimming, mapping, and signal tracks (bigWig) for plus and minus strands using scaled (based on mappability information) or unscaled read count patterns.


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

User interface

PEPPRO is a python script that runs on the command line (See usage). It can also read projects in PEP format. This means that PEPPRO 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.