immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

immuneSIM enables in silico generation of single and paired chain human and mouse B- and T-cell repertoires with user-defined tunable properties to provide the user with experimental-like (or aberrant) data to benchmark their repertoire analysis methods.

High frequency of shared clonotypes in human B cell receptor repertoires

The human genome contains approximately 20 thousand protein-coding genes1, but the size of the collection of antigen receptors of the adaptive immune system that is generated by the recombination of gene segments with non-templated junctional additions (on B cells) is unknown—although it is certainly orders of magnitude larger.

HereReproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (13). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail.

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Antigen specificity is a cardinal feature of adaptive immunity that underlies immune homeostasis and control of pathogenic attack in higher vertebrates.

Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping

Analysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding immunoglobulin genes is incomplete, resulting in conflicting VDJ gene assignments and biased genotype and haplotype inference. 

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