ArticleGenome biology2019
RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 422 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
422 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
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- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Dual-reference projection defines a callable core and reference-sensitive shell in a Qiantang River Megalobrama draft assembly.Functional & integrative genomics · 2026Article
- Convergent elevation of mitochondrial proton leakage improves thermogenesis in honeybees.Molecular biology and evolution · 2026Article
- Unheralded high MHC class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing.Science advances · 2026Article
- Complete genome sequence of the goatpox virus vaccine isolate LRIGP01.Microbiology resource announcements · 2026Article
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- Comparative genomic and functional insights into life-cycle plasticity and host adaptation in a wild Nippostrongylus brasiliensis strain from Guangzhou.BMC genomics · 2026Article
- Pan-genome based on chromosome sequences of wild and cultivated Agaricus bisporus.Scientific data · 2026Article
- Development of novel Aotus nancymaae non-human primate model for the evaluation of Plasmodium vivax blood stage vaccines and immunoprophylactics.Malaria journal · 2026Article
- Reference genome of an irruptive migrant, the pine siskin (Spinus pinus).The Journal of heredity · 2026Article
- Resolving repetitive and telomeric regions through a high-contiguity genome assembly of the African Turquoise killifish.Genes & genomics · 2026Article
- Abscisic Acid Induces Triacylglycerol Accumulation and Lipid Remodelling in Chloroplast-Containing Green Tissues of Lemna minor.Plant, cell & environment · 2026Article
- Genomic sequence and structural variations accumulating between laboratory lineages of wild typebioRxiv : the preprint server for biology · 2026Article
- Complete genome sequence of a circulating foot-and-mouth disease virus serotype A isolated from recent outbreaks in Bangladesh.Microbiology resource announcements · 2026Article
362 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO .
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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.