OMSim: a simulator for optical map data

Abstract

MOTIVATION: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire genome. In turn, these optical maps can be used to validate or improve de novo genome assembly projects or to detect large-scale structural variation in genomes. Simulated optical map data can assist in the development and benchmarking of tools that operate on those data, such as alignment and assembly software. Additionally, it can help to optimize the experimental setup for a genome of interest. Such a simulator is currently not available. RESULTS: We have developed a simulator, OMSim, that produces synthetic optical map data that mimics real Bionano Genomics data. These simulated data have been tested for compatibility with the Bionano Genomics Irys software system and the Irys-scaffolding scripts. OMSim is capable of handling very large genomes (over 30 Gbp) with high throughput and low memory requirements. AVAILABILITY AND IMPLEMENTATION: The Python simulation tool and a cross-platform graphical user interface are available as open source software under the GNU GPL v2 license ( http://www.bioinformatics.intec.ugent.be/omsim ). CONTACT: jan.fostier@ugent.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.