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Article
Open AccessThe complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked ...
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Article
Open AccessThe variation and evolution of complete human centromeres
Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolut...
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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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Article
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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Article
The complete sequence of a human Y chromosome
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, mo...
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Article
Open AccessRecombination between heterologous human acrocentric chromosomes
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of...
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Open AccessA draft human pangenome reference
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These...
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Article
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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Open AccessSemi-automated assembly of high-quality diploid human reference genomes
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not repres...
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Article
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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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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Article
The Human Pangenome Project: a global resource to map genomic diversity
The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a si...
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Open AccessAuthor Correction: Improved reference genome of the arboviral vector Aedes albopictus
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Open AccessEvolutionary and biomedical insights from a marmoset diploid genome assembly
The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning a...
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Article
Open AccessThe structure, function and evolution of a complete human chromosome 8
The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human c...
