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.

The simulation algorithm encompasses an in-silico VDJ recombination process with on-the-go detailed annotation of the generated sequences and if enabled by the user somatic hypermutation (SHM) and sequence motif implantation. The user-definable parameters are: Clone count distribution, Germline Gene Usage, Insertion and Deletion Occurrence, SHM likelihood and Motif Implantation.