ArticleGenome biology2016
OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.BMC genomics · 2026Article
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
- Maptcha: an efficient parallel workflow for hybrid genome scaffolding.BMC bioinformatics · 2024Article
- An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda, Md.) · 2023Article
- ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads.Current protocols · 2023Article
- An improved reference genome forFrontiers in plant science · 2023Article
- Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine.mSystems · 2022Article
- Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects.Nature microbiology · 2022Article
- RegScaf: a regression approach to scaffolding.Bioinformatics (Oxford, England) · 2022Article
- SWALO: scaffolding with assembly likelihood optimization.Nucleic acids research · 2021Article
- LongStitch: high-quality genome assembly correction and scaffolding using long reads.BMC bioinformatics · 2021Article
- A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat.Ecology and evolution · 2021Article
- Whole-Genome Sequencing Analysis of Salmonella Isolates from Poultry Farms, a Slaughterhouse, and Retail Stalls in Thailand.Microbiology resource announcements · 2021Article
- Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae).Scientific reports · 2021Article
- The genome sequence of the Australian filarial nematode,Wellcome open research · 2021Article
- Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome.Genome biology and evolution · 2020Article
- Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.Nature medicine · 2020Article
- TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools.Genome biology · 2019Article
- LRScaf: improving draft genomes using long noisy reads.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.
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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.