ArticleGenome research2018
Chromosome assembly of large and complex genomes using multiple references.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 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.
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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.
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Who cites it
70 citing papers in PubMed, 122 citations in OpenAlex.
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- Rapid evolution driven by translocation-associated selection during meiosis.EMBO reports · 2026Article
- Comprehensive genomic characterization of multidrug-resistantFrontiers in microbiology · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Comparison and Analysis of the Genomes of Three Strains ofMicroorganisms · 2025Article
- Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.Functional & integrative genomics · 2025Review
- Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti.PLoS genetics · 2025Article
- Scaffolded and annotated nuclear and organelle genomes of the North American brown algaFrontiers in genetics · 2025Article
- Bank vole genomics links determinate and indeterminate growth of teeth.BMC genomics · 2024Article
- The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera.Genome biology and evolution · 2024Article
- Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.G3 (Bethesda, Md.) · 2024Article
- A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.Journal of clinical microbiology · 2024Article
- Vole genomics links determinate and indeterminate growth of teeth.bioRxiv : the preprint server for biology · 2024Article
- A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes.Nature communications · 2024Article
- A region of suppressed recombination misleads neoavian phylogenomics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome.Genome biology and evolution · 2024Article
- Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.Nucleic acids research · 2024Article
- 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
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
Abstract
Despite the rapid development of sequencing technologies, the assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout 2, a reference-assisted assembly tool that works for large and complex genomes. By taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout 2 infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. By using Ragout 2, we transformed NGS assemblies of 16 laboratory mouse strains into sets of complete chromosomes, leaving <5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long Pacific Biosciences (PacBio) reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. We applied Ragout 2 to the
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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.