ArticleNature communications2014
High-quality genome (re)assembly using chromosomal contact data.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
What it found
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Who cites it
83 citing papers in PubMed.
- Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization.G3 (Bethesda, Md.) · 2026Article
- Interchromosomal Translocations and Large Deletions Drive the Evolution of the Outlier Chromosome in the Smallest Photosynthetic Eukaryote.Genome biology and evolution · 2026Article
- A chromosome-level genome assembly of the Fusarium oxysporum biocontrol strain FO12.Scientific data · 2026Article
- Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.Genome biology · 2026Article
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- N-acetylglucosamine sensing in the filamentous soil fungus Trichoderma reesei.The FEBS journal · 2025Article
- A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic acids research · 2024Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Article
- Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth.Research square · 2024Article
- Chromosome-scale assembly of the streamlined picoeukaryoteMicrobial genomics · 2024Article
- Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni.BMC genomics · 2024Article
- Orchestrating chromosome conformation capture analysis with Bioconductor.Nature communications · 2024Article
- A chromosome-scale genome assembly of mungbean (PeerJ · 2024Article
- Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads.Frontiers in bioinformatics · 2024Article
- Article
- Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.Nature genetics · 2023Article
- Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes.Nature communications · 2022Article
- The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins.Genome biology and evolution · 2022Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Closing gaps in draft genome assemblies can be costly and time-consuming, and published genomes are therefore often left 'unfinished.' Here we show that genome-wide chromosome conformation capture (3C) data can be used to overcome these limitations, and present a computational approach rooted in polymer physics that determines the most likely genome structure using chromosomal contact data. This algorithm--named GRAAL--generates high-quality assemblies of genomes in which repeated and duplicated regions are accurately represented and offers a direct probabilistic interpretation of the computed structures. We first validated GRAAL on the reference genome of Saccharomyces cerevisiae, as well as other yeast isolates, where GRAAL recovered both known and unknown complex chromosomal structural variations. We then applied GRAAL to the finishing of the assembly of Trichoderma reesei and obtained a number of contigs congruent with the know karyotype of this species. Finally, we showed that GRAAL can accurately reconstruct human chromosomes from either fragments generated in silico or contigs obtained from de novo assembly. In all these applications, GRAAL compared favourably to recently published programmes implementing related approaches.
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