[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 …

Twenty years of plant genome sequencing: achievements and challenges

Y Sun, L Shang, QH Zhu, L Fan, L Guo - Trends in Plant Science, 2022 - cell.com
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant
reference genome, in December 2000 heralded the beginning of the plant genome era …

[HTML][HTML] MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

M Uliano-Silva, JGRN Ferreira, K Krasheninnikova… - BMC …, 2023 - Springer
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb)
and highly accurate (> Q20). Because of these properties, they have revolutionised genome …

[HTML][HTML] 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 …

[HTML][HTML] Graph pangenome captures missing heritability and empowers tomato breeding

Y Zhou, Z Zhang, Z Bao, H Li, Y Lyu, Y Zan, Y Wu… - Nature, 2022 - nature.com
Missing heritability in genome-wide association studies defines a major problem in genetic
analyses of complex biological traits,. The solution to this problem is to identify all causal …

[HTML][HTML] Genome evolution and diversity of wild and cultivated potatoes

D Tang, Y Jia, J Zhang, H Li, L Cheng, P Wang, Z Bao… - Nature, 2022 - nature.com
Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the
vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances …

[HTML][HTML] Ancient gene linkages support ctenophores as sister to other animals

DT Schultz, SHD Haddock, JV Bredeson, RE Green… - Nature, 2023 - nature.com
A central question in evolutionary biology is whether sponges or ctenophores (comb jellies)
are the sister group to all other animals. These alternative phylogenetic hypotheses imply …

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 …

[HTML][HTML] A complete telomere-to-telomere assembly of the maize genome

J Chen, Z Wang, K Tan, W Huang, J Shi, T Li, J Hu… - Nature …, 2023 - nature.com
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of
genomic research. Through generating deep coverage ultralong Oxford Nanopore …

Protein-to-genome alignment with miniprot

H Li - Bioinformatics, 2023 - academic.oup.com
Motivation Protein-to-genome alignment is critical to annotating genes in non-model
organisms. While there are a few tools for this purpose, all of them were developed over 10 …