scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

Single cell chromatin accessibility sequencing (scCAS) has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. The development of several experimental protocols has led to a rapid accumulation of scCAS data. In contrast, there is a lack of open-source software tools for comprehensive processing, analysis and visualization of scCAS data generated using all existing experimental protocols. Here we present scATAC-pro for quality assessment, analysis and visualization of scCAS data. scATAC-pro provides flexible choice of methods for different data processing and analytical tasks, with carefully curated default parameters. A range of quality control metrics are computed for several key steps of the experimental protocol. scATAC-pro generates summary reports for both quality assessment and downstream analysis. It also provides additional utility functions for generating input files for various types of downstream analyses and data visualization. With the rapid accumulation of scCAS data, scATAC-pro will facilitate studies of epigenomic heterogeneity in healthy and diseased tissues.