ReviewThe Plant cell2018
Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping.
Review in The Plant cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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
21 citing papers in PubMed.
- A genome sequence and efficient CRISPR/Cas9 gene editing tools for the solanaceous specialist pest Tetranychus evansi.Insect biochemistry and molecular biology · 2026Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Spatial mapping of the DNA adducts in cancer.DNA repair · 2023Review
- Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions.Plants (Basel, Switzerland) · 2023Article
- Chromosome-Level Genome Assembly of a FragrantInternational journal of molecular sciences · 2022Article
- MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences.Journal of molecular biology · 2022Article
- gcaPDA: a haplotype-resolved diploid assembler.BMC bioinformatics · 2022Article
- Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.Molecular ecology resources · 2021Article
- Long-read human genome sequencing and its applications.Nature reviews. Genetics · 2020Review
- Centromere studies in the era of 'telomere-to-telomere' genomics.Experimental cell research · 2020Review
- PACVr: plastome assembly coverage visualization in R.BMC bioinformatics · 2020Article
- Gapless assembly of maize chromosomes using long-read technologies.Genome biology · 2020Article
- A platinum standard pan-genome resource that represents the population structure of Asian rice.Scientific data · 2020Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
- Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice.Frontiers in plant science · 2020Review
- Till 2018: a survey of biomolecular sequences in genusJournal of ginseng research · 2020Review
- Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize.The Plant cell · 2019Article
- The Genome Sequence ofFrontiers in plant science · 2019Article
- An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.Scientific reports · 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
Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.
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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.