Summary: We introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated. BUStools is a suite of tools for working with BUS files and facilitates rapid quantification and analysis of single-cell RNA-seq data. The BUS format therefore makes possible the development of modular, technology-specific and robust workflows for single-cell RNA-seq analysis. Availability and implementation: http://BUStools.github.io/ and http://pachterlab.github.io/kallisto/singlecell.html. Supplementary information: Supplementary data are available at Bioinformatics online.
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