Results 11 to 20 of about 138,057 (371)

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification [PDF]

eLife, 2020
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a ...
Barton, Geoffrey J., Gould, Peter D., Hall, Anthony J. W., Knop, Katarzyna, Mackinnon, Katarzyna, Parker, Matthew T., Schurch, Nicholas J., Sherwood, Anna V., Simpson, Gordon G.   +8 more
core   +4 more sources

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Nature Methods, 2022
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes.
M. Sereika, R. Kirkegaard, S. Karst, T. Michaelsen, E. A. Sørensen, R. Wollenberg, M. Albertsen   +6 more
semanticscholar   +1 more source

Efficient assembly of nanopore reads via highly accurate and intact error correction

Nature Communications, 2021
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences.
Ying Chen, Fan Nie, Shang-Qian Xie, Yingfeng Zheng, Qi Dai, Thomas Bray, Yaoxin Wang, Jian-feng Xing, Zhiyong Huang, De-Peng Wang, Li-Juan He, F. Luo, Jianxin Wang, Yizhi Liu, Chuan-Le Xiao   +14 more
semanticscholar   +1 more source

Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing

Nature Biotechnology, 2023
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking.
M. Lucas, Leszek P. Pryszcz, Rebeca Medina Amezcua, Ivan Milenkovic, Noelia Camacho, V. Marchand, Y. Motorin, L. Ribas de Pouplana, E. Novoa   +8 more
semanticscholar   +1 more source

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling

Applied and Environmental Microbiology, 2023
The long-read amplicon provides a species-level solution for the community. With the improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) R10.4.1 has been substantially enhanced, with an average of approximately 99%.
Tianyuan Zhang, Hanzhou Li, Silin Ma, Jian Cao, Hao Liao, Qiaoyun Huang, Wenli Chen   +6 more
semanticscholar   +1 more source

Enzyme-less nanopore detection of post-translational modifications within long polypeptides

bioRxiv, 2023
Means to sequence DNA and RNA quickly and cheaply have revolutionized biology and medicine. The ability to analyse cellular proteins and their millions of variants would be an advance of comparable importance, but requires a fresh technical approach.
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie J. Board, Mercedes Romero-Ruiz, S. Garcia-Manyes, Yujia Qing, H. Bayley   +6 more
semanticscholar   +1 more source

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Nature Biotechnology, 2020
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen M. Bosworth, J. Armstrong, Kristof Tigyi, Nicholas W. Maurer, S. Koren, F. Sedlazeck, T. Marschall, Simon Mayes, Vania Costa, J. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katherine M. Munson, Mitchell R. Vollger, J. Monlong, Erik K. Garrison, E. Eichler, S. Salama, D. Haussler, R. Green, M. Akeson, A. Phillippy, K. Miga, P. Carnevali, Miten Jain, Benedict Paten   +31 more
semanticscholar   +1 more source

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required

Microorganisms, 2023
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows.
Márton Szoboszlay, Laetitia Schramm, David Pinzauti, J. Scerri, A. Sandionigi, Manuele Biazzo   +5 more
semanticscholar   +1 more source

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Genome Biology, 2019
Basecalling, the computational process of translating raw electrical signal to nucleotide sequence, is of critical importance to the sequencing platforms produced by Oxford Nanopore Technologies (ONT).
R. Wick, L. Judd, K. Holt
semanticscholar   +1 more source

MoS2 nanopore identifies single amino acids with sub-1 Dalton resolution

Nature Communications, 2023
The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores.
Fushi Wang, Chunxiao Zhao, Pinlong Zhao, Fanfan Chen, Dan Qiao, Jiandong Feng   +5 more
semanticscholar   +1 more source