immuneSIM

Tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking | The goal of the immuneSIM simulation is to in silico generate human and mouse B- and T-cell repertoires with user-defined properties to provide the user with custom native or aberrant immune receptor sequence repertoires to benchmark their repertoire analysis tools. The simulation algorithm implements an in silico VDJ recombination process with on-the-go annotation of the generated sequences and if enabled by the user somatic hypermutation (SHM) and motif implantation. With a wide range of user-modifiable parameters, a uniquely diverse set of repertoires can be created. The parameters include: Clone count distribution, Germline Gene Usage, Insertion and Deletion Occurrence, SHM likelihood and Motif Implantation