Abstract
Single cell chromatin accessibility sequencing (scCAS) has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. A number of experimental protocols have been developed for scCAS. However, there is a lack of flexible and 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 processing, analyzing and visualization of scCAS data. scATAC-pro provides flexible choice of methods for different data processing and analytical tasks, with carefully curated default parameters. scATAC-pro also generates detailed data quality and analysis reports in html format and provides interface to visualization software and additional utility functions for various types of downstream analyses.