Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with VDJer

We present here V’DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V’DJer’s ability to accurately reconstruct BCR repertoires from short read mRNA-seq data.
Availability and Implementation: V’DJer is implemented in C/C ++, freely available for academic use and can be downloaded from Github: https://github.com/mozack/vdjer
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Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - December 18, 2016 Category: Bioinformatics Authors: Mose, L. E., Selitsky, S. R., Bixby, L. M., Marron, D. L., Iglesia, M. D., Serody, J. S., Perou, C. M., Vincent, B. G., Parker, J. S. Tags: SEQUENCE ANALYSIS Source Type: research