[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

Next-generation sequencing technologies: An overview

T Hu, N Chitnis, D Monos, A Dinh - Human Immunology, 2021 - Elsevier
Since the days of Sanger sequencing, next-generation sequencing technologies have
significantly evolved to provide increased data output, efficiencies, and applications. These …

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 …

A draft human pangenome reference

WW Liao, M Asri, J Ebler, D Doerr, M Haukness… - Nature, 2023 - nature.com
Abstract Here the Human Pangenome Reference Consortium presents a first draft of the
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …

Detection of mosaic and population-level structural variants with Sniffles2

M Smolka, LF Paulin, CM Grochowski, DW Horner… - Nature …, 2024 - nature.com
Calling structural variations (SVs) is technically challenging, but using long reads remains
the most accurate way to identify complex genomic alterations. Here we present Sniffles2 …

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 …

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 …

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

H Cheng, GT Concepcion, X Feng, H Zhang, H Li - Nature methods, 2021 - nature.com
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence
variations in a genome. However, existing algorithms either collapse heterozygous alleles …

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

K Shafin, T Pesout, PC Chang, M Nattestad… - Nature …, 2021 - nature.com
Long-read sequencing has the potential to transform variant detection by reaching currently
difficult-to-map regions and routinely linking together adjacent variations to enable read …