Variant calling and benchmarking in an era of complete human genome sequences

ND Olson, J Wagner, N Dwarshuis, KH Miga… - Nature Reviews …, 2023 - nature.com
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …

The complete sequence of a human Y chromosome

A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor… - Nature, 2023 - nature.com
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 …

Telomere-to-telomere assembly of diploid chromosomes with Verkko

M Rautiainen, S Nurk, BP Walenz, GA Logsdon… - Nature …, 2023 - nature.com
Abstract 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 …

The complete sequence of a human genome

S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze… - Science, 2022 - science.org
Since its initial release in 2000, the human reference genome has covered only the
euchromatic fraction of the genome, leaving important heterochromatic regions unfinished …

Complete genomic and epigenetic maps of human centromeres

N Altemose, GA Logsdon, AV Bzikadze, P Sidhwani… - Science, 2022 - science.org
Existing human genome assemblies have almost entirely excluded repetitive sequences
within and near centromeres, limiting our understanding of their organization, evolution, and …

A complete reference genome improves analysis of human genetic variation

S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate… - Science, 2022 - science.org
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200
million base pairs of sequence, corrects thousands of structural errors, and unlocks the most …

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

SJ Hoyt, JM Storer, GA Hartley, PGS Grady… - Science, 2022 - science.org
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic
innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such …

The genetic and epigenetic landscape of the Arabidopsis centromeres

M Naish, M Alonge, P Wlodzimierz, AJ Tock… - Science, 2021 - science.org
INTRODUCTION The centromeres of eukaryotic chromosomes assemble the multiprotein
kinetochore complex and thereby position attachment to the spindle microtubules, allowing …

Long-read mapping to repetitive reference sequences using Winnowmap2

C Jain, A Rhie, NF Hansen, S Koren, AM Phillippy - Nature Methods, 2022 - nature.com
Abstract Approximately 5–10% of the human genome remains inaccessible due to the
presence of repetitive sequences such as segmental duplications and tandem repeat arrays …

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Y Deng, S Liu, Y Zhang, J Tan, X Li, X Chu, B Xu… - Molecular plant, 2022 - cell.com
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …