25 Result(s)
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Article
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
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Article
Open AccessHigh-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address varia...
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Article
Improved sequence map** using a complete reference genome and lift-over
Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, th...
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Telomere-to-telomere assembly of diploid chromosomes with Verkko
The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford N...
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensiv...
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Open AccessA haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modificatio...
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Article
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplicatio...
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Article
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Variant calling has been widely used for genoty** and for improving the consensus accuracy of long-read assemblies. Variant calls are commonly hard-filtered with user-defined cutoffs. However, it is impossib...
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Article
Long-read map** to repetitive reference sequences using Winnowmap2
Approximately 5–10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often y...
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Author Correction: A robust benchmark for detection of germline large deletions and insertions
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
A robust benchmark for detection of germline large deletions and insertions
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine r...
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Article
Open AccessGenomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
The New World Screwworm fly, Cochliomyia hominivorax, is a major pest of livestock in South America and Caribbean. However, few genomic resources have been available for this species. A genome of 534 Mb was assem...
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Open AccessEvolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level...
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Article
Open AccessNew insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific g...
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Article
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of...
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Article
Reply to ‘Errors in long-read assemblies can critically affect protein prediction’
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Article
De novo assembly of haplotype-resolved genomes with trio binning
Trio binning assembles both haplotypes of a genome by combining long-read sequence data with short-read data from both parents.
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Open AccessNanopore sequencing and assembly of a human genome with ultra-long reads
A human genome is sequenced and assembled de novo using a pocket-sized nanopore device.
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Article
Correction: Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Nat. Biotechnol. 33, 623–630 (2015); published online 25 May 2015; corrected after print 6 October 2015 In the version of this article initially published, equation 9 appeared incorrectly as: The equation has ...
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Article
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
An assembly algorithm that overlaps noisy long reads enables accurate and fast assembly of large genomes from single-molecule real-time sequences.
