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

Genome Biol. 2020 Apr 20;21(1):94. doi: 10.1186/s13059-020-02008-0.


Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at

Keywords: Bioinformatics; Chromatin accessibility; Genomics; Single cell.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / metabolism*
  • Gene Ontology
  • Humans
  • Protein Footprinting
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / standards
  • Single-Cell Analysis / methods*
  • Single-Cell Analysis / standards
  • Software*
  • Transcription Factors / metabolism
  • Workflow


  • Chromatin
  • Transcription Factors