PEPPRO

Quality control and processing of nascent RNA profiling data. 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.