ArticleBioinformatics (Oxford, England)2021
Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed, 8 citations in OpenAlex.
- 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
- A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.Molecular biology and evolution · 2025Article
- AsmMix: an efficient haplotype-resolved hybridFrontiers in genetics · 2024Article
- MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads.iMeta · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
Abstract
motivationAchieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging.
resultsTo address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assemble the parent-specific haplotypes. We applied HAST to cobarcoded second-generation sequencing data from an Asian individual, resulting in a haplotype assembly covering 94.7% of the reference genome with a scaffold N50 longer than 11 Mb. The high haplotyping precision (∼99.7%) and recall (∼95.9%) represents a substantial improvement over the commonly used tool for assembling cobarcoded reads (Supernova), and is comparable to a trio-binning-based third generation long-read-based assembly method (TrioCanu) but with a significantly higher single-base accuracy [up to 99.99997% (Q65)]. This makes HAST a superior tool for accurate haplotyping and future haplotype-based studies. AVAILABILITY AND IMPLEMENTATION: The code of the analysis is available at https://github.com/BGI-Qingdao/HAST. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Identifiers
What OpenQuestion holds
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.