ArticleNature biotechnology2018
De novo assembly of haplotype-resolved genomes with trio binning.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 297 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
297 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives.Plant communications · 2022Pooled it
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- Identification of carnivory in the flowering plant Saxifraga via multidisciplinary evidence.Nature communications · 2026Article
- Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding.Nature communications · 2026Article
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- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-resolved methylomes reveal parent-of-origin DNA methylation imbalance in autism spectrum disorder.Science advances · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- High quality genome assemblies of African cattle breeds using PacBio HiFi sequencing.Scientific data · 2026Article
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- LORA: a polymorphic multi-sample long read assembly pipeline.NAR genomics and bioinformatics · 2026Article
- New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.BMC genomics · 2026Article
- Extensive variation between chromosomes of North American and European hop.Nature communications · 2026Article
- Haplotype-resolved genome assemblies for the New World screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), using the trio binning approach.G3 (Bethesda, Md.) · 2026Article
237 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
10 authors.
Funding
Abstract
Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly. In contrast with prior approaches, the effectiveness of our method improved with increasing heterozygosity. Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. We used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches. We sequenced an F1 cross between the cattle subspecies Bos taurus taurus and Bos taurus indicus and completely assembled both parental haplotypes with NG50 haplotig sizes of >20 Mb and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We suggest that trio binning improves diploid genome assembly and will facilitate new studies of haplotype variation and inheritance.
Identifiers
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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.