ArticleBioinformatics (Oxford, England)2017
OMSim: a simulator for optical map data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 20 citations in OpenAlex.
- Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.BMC bioinformatics · 2021Article
- Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.Algorithms for molecular biology : AMB · 2021Article
- AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.Nature communications · 2020Article
- Fast and accurate correction of optical mapping data via spaced seeds.Bioinformatics (Oxford, England) · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
- Error correcting optical mapping data.GigaScience · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe 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.
resultsWe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.