Fig. 1.

Overview of scRNA-seq preprocessing workflows and study design. (A) A typical preprocessing workflow begins with raw sequences in FASTQ files that are subject to cell barcode (CB) detection, alignment, UMI correction, count matrix generation, and quality control. (B) Summary of benchmarking study, showing the datasets analyzed, the selected preprocessing workflows and methods for normalization and clustering that were compared. Workflows and methods used in analysis are listed in boxes with solid borders, while evaluation metrics are shown in boxes with dashed borders. In total, 3870 combinations of datasets × preprocessing workflows × downstream analysis methods were generated in this study