PEP compatible

PEPPRO is a pipeline for nascent RNA sequencing data. It can process PRO-seq, GRO-seq, and ChRO-seq data and is optimized on unique features of nascent RNA to be fast and accurate. It performs variable-length UMI adapter removal, read deduplication, trimming, mapping, QC, and signal tracks (bigWig) for plus and minus strands using mappability-scaled or unscaled read counts.


PEPPRO produces quality control plots, statistics, and data formats to set the stage for project-specific 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.
  • Processed data: Several bigWig signal tracks (plus and minus stranded), with options to produce: smoothed signal; exact (nucleotide-resolution) RNA polymerase position signal; or nucleotide-resolution signal corrected for enzymatic sequence bias.

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.


If you find PEPPRO useful in your research, please cite:

Smith, J.P., Dutta, A.B., Sathyan, K.M. et al. PEPPRO: quality control and processing of nascent RNA profiling data. Genome Biol 22, 155 (2021).