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.

Table of Contents

Contents:

• Quickstart guide
  • Overview
  • Workflow of the quickstart simulation
• Simulation
  • The workflow of a standard immuneSIM simulation
  • in-silico VDJ recombination
  • Post simulation modifications
  • Report generation
  • Flowchart immuneSIM
• Parameters
  • Parameter 1: Choice of model (species and receptor)
  • Parameter 2: Repertoire size (Number of simulated sequences)
  • Parameter 3: Maximal and minimal amino acid CDR3 length
  • Parameter 4: Clone count distribution
  • Parameter 5: V,D,J germline gene frequencies
  • Parameter 6: Insertion and deletions
  • Parameter 7: Somatic hypermutation likelihood
  • Parameter 8: Frequency update threshold
  • Parameter 9: Random repertoires
  • Parameter 10: Motif implantation
  • Parameter 11: Sequence similarity
  • Parameter 12: Codon bias
  • Table: Reference datasets
• Somatic hypermutation
  • Somatic hypermutation model
• Motif implantation
  • Parameter: motif
  • Parameter: fixed_pos
• Report generation
  • Single repertoire
  • Comparative
• Acknowledgments