ArticleBMC bioinformatics2020
Optical map guided genome assembly.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Evidence supporting the first secondary chromosome in Actinobacteria as a hallmark of theMicrobial genomics · 2026Article
- Benchmarking of bioinformatics tools for the hybridComputational and structural biotechnology journal · 2025Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.BMC genomics · 2024Article
- Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species.BMC genomics · 2023Article
- The first complete genome of the simian malaria parasite Plasmodium brasilianum.Scientific reports · 2022Article
- Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki.G3 (Bethesda, Md.) · 2022Article
- HGGA: hierarchical guided genome assembler.BMC bioinformatics · 2022Article
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- An Overview of the Genetics and Genomics of theFrontiers in plant science · 2021Review
Corrections and comments
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly.
resultsWe propose OPTICALKERMIT which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OPTICALKERMIT produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads.
conclusionsOPTICALKERMIT successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.
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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.