BASIC: BCR assembly from single cells

Motivation: The B‐cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA‐sequencing (RNA‐seq) have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full‐length heavy and light chain sequences from single cell RNA‐seq (scRNA‐seq) in B cells has been largely unstudied. Results: We developed a new software tool, BASIC, which allows investigators to use scRNA‐seq for assembling BCR sequences at single‐cell resolution. To demonstrate the utility of our software, we subjected nearly 200 single human B cells to scRNA‐seq, assembled the full‐length heavy and the light chains, and experimentally confirmed these results by using single‐cell primer‐based nested PCRs and Sanger sequencing. Availability and Implementation: http://ttic.uchicago.edu/˜aakhan/BASIC Contact: aakhan@ttic.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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