ArticleG3 (Bethesda, Md.)2020
Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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.
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Who cites it
29 citing papers in PubMed.
- Haplotype-phased 'Ottawa 3' genome unravels differential reaction of apple rootstock roots to mixed viral infection.The Plant journal : for cell and molecular biology · 2026Article
- Hemoglobin-Gene Cluster Deletions in Antarctic White-Blooded Icefishes Facilitated by Transposable Elements.Genome biology and evolution · 2025Article
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis).G3 (Bethesda, Md.) · 2025Article
- Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly.G3 (Bethesda, Md.) · 2025Article
- High-quality chromosome-level genome assembly of femaleHeliyon · 2024Article
- Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum.Communications biology · 2024Article
- De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation.BMC biology · 2024Article
- Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation.Genome biology and evolution · 2024Article
- De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus.GigaScience · 2024Article
- Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes.Molecular biology and evolution · 2023Article
- Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.G3 (Bethesda, Md.) · 2023Article
- Sablefish (Anoplopoma fimbria) chromosome-level genome assembly.G3 (Bethesda, Md.) · 2023Article
- High resolution genomes of multipleGenome research · 2023Article
- Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case ofAnimals : an open access journal from MDPI · 2023Article
- An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly.G3 (Bethesda, Md.) · 2022Article
- HGGA: hierarchical guided genome assembler.BMC bioinformatics · 2022Article
- Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Genome of the Poecilogonous Annelid Streblospio benedicti.Genome biology and evolution · 2022Article
- A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush).Molecular ecology resources · 2022Article
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Authors and funding
3 authors.
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Abstract
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.
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