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.

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