39 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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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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Article
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 AccessFalse gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as com...
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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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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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Open AccessAuthor Correction: Improved reference genome of the arboviral vector Aedes albopictus
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Article
Open AccessComplete vertebrate mitogenomes reveal widespread repeats and gene duplications
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
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Article
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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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 AccessMerqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation...
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Open AccessImproved reference genome of the arboviral vector Aedes albopictus
The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary a...
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Open AccessStrains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed si...
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Open AccessMash Screen: high-throughput sequence containment estimation for genome discovery
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. H...
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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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Open AccessAssignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read ...
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Reply to ‘Errors in long-read assemblies can critically affect protein prediction’
