ArticleBioinformatics (Oxford, England)2015
Misassembly detection using paired-end sequence reads and optical mapping data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.Algorithms for molecular biology : AMB · 2021Article
- Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2021Article
- 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
- LRScaf: improving draft genomes using long noisy reads.BMC genomics · 2019Article
- Comparative Analysis ofInsects · 2019Article
- Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.GigaScience · 2019Article
- Error correcting optical mapping data.GigaScience · 2018Article
- Disentangling the Causes for Faster-X Evolution in Aphids.Genome biology and evolution · 2018Article
- misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny.Genomics & informatics · 2017Article
- Succinct colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2017Article
- OMSim: a simulator for optical map data.Bioinformatics (Oxford, England) · 2017Article
- Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan.BMC genomics · 2016Article
- Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products.Marine drugs · 2016Review
- Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.BMC genomics · 2016Article
- Analysis of single nucleic acid molecules in micro- and nano-fluidics.Lab on a chip · 2016Review
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Authors and funding
4 authors.
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Abstract
motivationA crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.
resultsOur results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine. Using the real optical mapping data, we correctly identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budgerigar. AVAILABILITY AND IMPLEMENTATION: misSEQuel can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/.
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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.