Fig. 1: Overview of UniverSC.

Given a pair of FASTQ files (R1 and R2), a genome reference (as required by Cell Ranger), and the name of the technology, UniverSC first runs a basic input curation (step-1). The curated input files are then adjusted for pipeline-specific modification (step-2) and subsequently reformatted to match the expected barcode and UMI lengths (step-3). In parallel, the barcode whitelist suited for the technology (if unspecified by the user) is determined (step-4), and the whitelist barcodes are modified to 16 bp (step-5). If the selected whitelist is different from the whitelist in place for Cell Ranger at the moment, the whitelist is replaced (step-6). Finally, the modified sample data is processed by Cell Ranger against the modified whitelist (step-7) to generate a standard output along with a summary file with per cell statistics.