ArticleBMC bioinformatics2022
EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends.
Article in BMC bioinformatics, 2022. 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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Who cites it
29 citing papers in PubMed.
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing.Communications biology · 2026Article
- The near telomere-to-telomere genome assembly and annotation of the Asian house shrew (Suncus murinus, Soricidae, Eulipotyphla).Scientific data · 2026Article
- Telomere-to-telomere genome assembly and comprehensive mutation library facilitate bitter gourd breeding and functional genomics research.Plant communications · 2026Article
- Improved Longan Genome Assembly Reveals Insights Into Flowering Mechanisms.Plant biotechnology journal · 2026Article
- The genomes of 5 mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification.GigaScience · 2026Article
- PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads.Briefings in bioinformatics · 2026Article
- Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.Nature communications · 2025Article
- Little millet genome reveals evolutionary insights into tetraploid structure and genetic basis of micronutrient density.Nature communications · 2025Article
- A chromosome-level genome assembly of Guimi No. 2 (Actinidia chinensis).Scientific data · 2025Article
- Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens).Scientific data · 2025Article
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
- A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.Nature genetics · 2025Article
- A chromosome-scale reference assembly of Vigna radiata enables delineation of centromeres and telomeres.Scientific data · 2025Article
- Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement.Plant communications · 2025Article
- A chromosome-scale reference genome of the Banna miniature inbred pig.Scientific data · 2024Article
- 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
- The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis.Plant communications · 2024Article
- Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding.Nature genetics · 2024Article
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10 authors.
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Abstract
backgroundThe application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding tools, which count Hi-C links between contigs using the whole or a large part of contig regions. As the Hi-C links of two adjacent contigs concentrate only at the neighbor ends of the contigs, larger contig size will reduce the power to differentiate adjacent (signal) and non-adjacent (noise) contig linkages, leading to a higher rate of mis-assembly.
resultsWe design and develop a novel Hi-C based scaffolding tool EndHiC, which is suitable to assemble large contigs into chromosomal-level scaffolds. The core idea behind EndHiC, which distinguishes it from other Hi-C scaffolding tools, is using Hi-C links only from the most effective regions of contig ends. By this way, the signal neighbor contig linkages and noise non-neighbor contig linkages are separated more clearly. Benefiting from the increased signal to noise ratio, the reciprocal best requirement, as well as the robustness evaluation, EndHiC achieves higher accuracy for scaffolding large contigs compared to existing tools. EndHiC has been successfully applied in the Hi-C scaffolding of simulated data from human, rice and Arabidopsis, and real data from human, great burdock, water spinach, chicory, endive, yacon, and Ipomoea cairica, suggesting that EndHiC can be applied to a broad range of plant and animal genomes.
conclusionsEndHiC is a novel Hi-C scaffolding tool, which is suitable for scaffolding of contig assemblies with contig N50 size near or over 10 Mb and N90 size near or over 1 Mb. EndHiC is efficient both in time and memory, and it is interface-friendly to the users. As more genome projects have been launched and the contig continuity constantly improved, we believe EndHiC has the potential to make a great contribution to the genomics field and liberate the scientists from labor-intensive manual curation works.
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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.