PT  - JOURNAL ARTICLE
AU  - Cédric R. Weber
AU  - Rahmad Akbar
AU  - Alexander Yermanos
AU  - Milena Pavlović
AU  - Igor Snapkov
AU  - Geir Kjetil Sandve
AU  - Sai T. Reddy
AU  - Victor Greiff
TI  - immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
AID  - 10.1101/759795
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 759795
4099  - http://biorxiv.org/content/early/2019/09/06/759795.short
4100  - http://biorxiv.org/content/early/2019/09/06/759795.full
AB  - Summary B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full length variable region immune receptor sequences. ImmuneSIM enables the tuning of the immune receptor features: (i) species and chain type (BCR, TCR, single, paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation, and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis, and machine learning methods for motif detection.Availability The package is available via https://github.com/GreiffLab/immuneSIM and will also be available at CRAN (submitted). The documentation is hosted at https://immuneSIM.readthedocs.io.Contact victor.greiff{at}medisin.uio, sai.reddy{at}ethz.ch