ReviewGigaScience2015
Using optical mapping data for the improvement of vertebrate genome assemblies.
Review in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.ACS omega · 2025Article
- The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus.Marine biotechnology (New York, N.Y.) · 2023Article
- A chromosome-level reference genome and pangenome for barn swallow population genomics.Cell reports · 2023Article
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- Chromosome-Level Genome Assembly of a FragrantInternational journal of molecular sciences · 2022Article
- Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern.Molecular ecology · 2021Article
- A single QTL with large effect is associated with female functional virginity in an asexual parasitoid wasp.Molecular ecology · 2021Article
- Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data.International journal of molecular sciences · 2021Article
- Review
- Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.G3 (Bethesda, Md.) · 2020Article
- Understanding Host-Pathogen Interactions inPlants (Basel, Switzerland) · 2020Review
- Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
- Long walk to genomics: History and current approaches to genome sequencing and assembly.Computational and structural biotechnology journal · 2020Review
- Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding.Animal genetics · 2019Review
- Improving draft genome contiguity with reference-derived in silico mate-pair libraries.GigaScience · 2018Article
- Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.BMC genomics · 2018Article
- Entropic trap purification of long DNA.Lab on a chip · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.
Indexed as
Identifiers
What OpenQuestion holds
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.