Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT


  • C.W. Hsu
  • R. Shahan
  • T.M. Nolan
  • P.N. Benfey
  • U. Ohler


  • STAR Protocols


  • STAR Protoc 3 (4): 101729


  • We describe a protocol to perform fast and non-arbitrary quality control of single-cell RNA sequencing (scRNA-seq) raw data using scKB and COPILOT. scKB is a wrapper script of kallisto and bustools for accelerated alignment and transcript count matrix generation, which runs significantly faster than the popular tool Cell Ranger. COPILOT then offers non-arbitrary background noise removal by comparing distributions of low-quality and high-quality cells. Together, this protocol streamlines the processing workflow and provides an easy entry for new scRNA-seq users. For complete details on the use and execution of this protocol, please refer to Shahan et al. (2022).