ArticleBioinformatics (Oxford, England)2017
OMBlast: alignment tool for optical mapping using a seed-and-extend approach.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing.Bioinformatics (Oxford, England) · 2026Article
- DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.ACS omega · 2025Article
- Extrachromosomal DNA in Cancer.Annual review of genomics and human genetics · 2022Review
- 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
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- nanotatoR: a tool for enhanced annotation of genomic structural variants.BMC genomics · 2021Article
- Signal-based optical map alignment.PloS one · 2021Article
- AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.Nature communications · 2020Article
- Optical map guided genome assembly.BMC bioinformatics · 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
- Genome rearrangements induce biofilm formation in Escherichia coli C - an old model organism with a new application in biofilm research.BMC genomics · 2019Article
- OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps.GigaScience · 2019Article
- A reference-grade wild soybean genome.Nature communications · 2019Article
- Genome maps across 26 human populations reveal population-specific patterns of structural variation.Nature communications · 2019Article
- Kohdista: an efficient method to index and query possible Rmap alignments.Algorithms for molecular biology : AMB · 2019Article
- Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data.Scientific reports · 2018Article
- Error correcting optical mapping data.GigaScience · 2018Article
- Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.PloS one · 2018Article
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Authors and funding
7 authors.
Funding
Abstract
Background: Optical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping. Results: Experiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also shows significant improvement when aligning data with SVs. Availability and Implementation: OMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast and run directly on machines equipped with a Java virtual machine. Contact: kevinyip@cse.cuhk.edu.hk and tf.chan@cuhk.edu.hk Supplementary Information: Supplementary data are available at Bioinformatics online.
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Registered trials
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.