ArticleNature communications2021
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 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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Who cites it
88 citing papers in PubMed, 130 citations in OpenAlex.
- Comparative genomics reveals lineage-associated structural variation and diversification in a barley fungal pathogen.The New phytologist · 2026Article
- Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing.Genes · 2026Review
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes.Nature communications · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states.Nature communications · 2026Article
- Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Targeted sequencing and iterative assembly of near-complete genomes.Nature communications · 2025Article
- A library of avian proteins improves palaeoproteomic taxonomic identification and reveals widespread intraspecies variability.Nature communications · 2025Article
- JG2: an updated version of the Japanese population-specific reference genome.Human genome variation · 2025Article
- Chromatin dynamics of a large-sized genome provides insights into polyphenism and X0 dosage compensation of locusts.Nature genetics · 2025Article
- High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning.BMC genomics · 2025Article
- The Genomic Basis of the Tristylous Floral Polymorphism: Evidence for a Role of Gene Duplications in a Region of Restricted Recombination.Molecular biology and evolution · 2025Article
- Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.Genome research · 2025Article
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
28 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
21 authors at 9 institutions in 3 countries.
Funding
Abstract
Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80-91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.
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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.