BASIC: BCR assembly from single cells

Bioinformatics. 2017 Feb 1;33(3):425-427. doi: 10.1093/bioinformatics/btw631.


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:∼aakhan/BASIC


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Gene Expression Profiling / methods*
  • Gene Expression Regulation
  • Humans
  • Receptors, Antigen, B-Cell / genetics*
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Software*


  • Receptors, Antigen, B-Cell