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BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing

By Ida Lindeman, Guy Emerton, Ludvig M. Sollid, Sarah A. Teichmann, Michael J. T. Stubbington

Posted 07 Sep 2017
bioRxiv DOI: 10.1101/185504 (published DOI: 10.1038/s41592-018-0082-3)

Reconstruction of antigen receptor sequences from single-cell RNA-sequencing (scRNA-seq) data allows the linking of antigen receptor usage to the full transcriptomic identity of individual B lymphocytes, without having to perform additional targeted repertoire sequencing (Rep-seq). Here we report BraCeR (freely available at https://github.com/teichlab/bracer/), an extension of TraCeR, for reconstruction of paired full-length B-cell receptor sequences and inference of clonality from scRNA-seq data. With an easy-to-use command-line interface, BraCeR provides a complete pipeline for clonal inference and lineage tracing of B cells. Raw scRNA-seq reads can be processed all the way to clonal networks and lineage trees, facilitating linkage of transcriptomic phenotype to the evolution of immunoglobulin sequences.

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