PEPATAC -- A robust ATAC-seq pipeline built on a loosely coupled modular framework

As chromatin accessibility data from ATAC-seq experiments become widespread, there is increasing need for standardized analysis pipelines. PEPATAC is an ATAC-seq pipeline that may be easily applied to 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. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. PEPATAC is built using a common project definition and other modular components that make it easy to analyze pipeline output using metadata APIs in R and Python. PEPATAC is a useful first step in universal data analysis for any ATAC-seq project.


Getting started

How-to guides

Example PEPATAC results