FetchPA: a guided, end-to-end solution for local ATAC-Seq data processing and analyses

Abstract

Local genome accessibility strongly correlates with activity of cis-regulatory elements, and Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq) has emerged as method of choice to profile chromatin accessibility in both healthy and pathogenic conditions. The introduction of streamlined protocols and manufacturer kits has made this technique accessible to labs of a variety of disciplines, background, and research interests. Many bioinformatics tools have been created for the quality control, mapping, and visualization of ATAC-seq data, however these tools require familiarity with shell scripting, version control, UNIX directory structure, Python and/or R. Several pipelines for the processing of ATAC-seq data have been developed, yet even with these tools, bioinformatic analyses represents a bottleneck between wet-lab protocol execution and graphical representation of differentially accessible regions. To address this problem, we assembled FetchPA, an intuitive pipeline which allows users with virtually no scripting and version control experience to install and manage all software for end-to-end analyses of ATAC-Seq data. FetchPA handles both local and public repository sources of sequencing data, executes standard QC benchmarks, and handles genome assembly and alignment using industry-standard PEPATAC pipeline. Further, it guides the user through the identification of differentially accessible regions and allows basic exploratory analyses via a dialogue interface. FetchPA operates in Windows Subsystem for Linux (WSL) and is installed via a single script that handles all individual tools, as well as their dependencies and updates, reference genome annotations and system resource allocation.