A software for inference of B-cell receptor (BCR) repertoires using short-read RNA sequencing data. V'DJer uses customized read extraction, assembly and V(D)J rearrangement detection and filtering to produce contigs representing the most abundant portions of the BCR. V’DJer allows for full inference of repertoire characteristics including variable and joining gene segment usage, population diversity, sequence sharing between populations, antigen binding region amino acid properties and motifs, clonal structure and somatic hypermutation in BCR repertoires.
Quantifies individual immune response based on a recombination landscape of genes encoding B and T cell receptors (BCR and TCR). ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. It is able to efficiently extract TCR- and BCR- derived reads from the RNA-Seq data and accurately assemble clonotypes (defined as clones with identical CDR3 amino acid sequences) and detect corresponding V(D)J recombinations. Using CAST clustering technique, ImReP is able to correct assembled clonotypes for PCR and sequencing errors.