Results 1 to 10 of about 33,843 (263)

Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies

Microbiology Spectrum, 2022
Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping.
Maisha F. Jabeen, Nicholas D. Sanderson, Dona Foster, Derrick W. Crook, Jennifer L. Cane, Catherine Borg, Clare Connolly, Samantha Thulborn, Ian D. Pavord, Paul Klenerman, Teresa L. Street, Timothy S. C. Hinks   +11 more
doaj   +3 more sources

MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads [PDF]

BMC Bioinformatics
Background The high error rate associated with Oxford Nanopore sequencing technology adversely affects demultiplexing. To improve demultiplexing and reduce unclassified reads from nanopore sequencing data, we developed MysteryMaster, a demultiplexer that
Abdolrahman Khezri, Sverre Branders, Anurag Basavaraj Bellankimath, Jawad Ali, Crystal Chapagain, Fatemeh Asadi, Manfred G. Grabherr, Rafi Ahmad   +7 more
doaj   +2 more sources

Understanding the Impact of Individual Nucleotide on Oxford Nanopore Current Signals With Interpretable Prediction Models [PDF]

Bioinformatics and Biology Insights
Oxford nanopore sequencing enabled real-time, long-read analysis of DNA by detecting ionic current signals associated with K-mer sequences. Although many studies analyzed sequence and modification detection, our understanding of how multiple nucleotides ...
Yenan Wang, Zhixing Wu, Jia Meng
doaj   +2 more sources

Oxford Nanopore MinION Sequencing and Genome Assembly

Genomics, Proteomics and Bioinformatics, 2016
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology ...
Hengyun Lu, Francesca Giordano, Zemin Ning   +2 more
exaly   +2 more sources

Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics. [PDF]

Int J Mol Sci
The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data.
Krivonos DV, Fedorov DE, Konanov DN, Vvedensky AV, Sonets IV, Korneenko EV, Speranskaya AS, Ilina EN.   +7 more
europepmc   +2 more sources

High-throughput Oxford Nanopore sequencing-based approach for the multilocus sequence typing analysis of large-scale avian Escherichia coli study in Mississippi

Poultry Science
: Avian pathogenic Escherichia coli (APEC) cause avian colibacillosis and accurately distinguishing infectious isolates is critical for controlling its transmission.
Linan Jia, Mark A Arick, Chuan-Yu Hsu
exaly   +3 more sources

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology [PDF]

PeerJ, 2022
Background Next Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading technologies currently being used by ...
Anna Czmil, Michal Wronski, Sylwester Czmil, Marta Sochacka-Pietal, Michal Cmil, Jan Gawor, Tomasz Wołkowicz, Dariusz Plewczynski, Dominik Strzalka, Michal Pietal   +9 more
doaj   +2 more sources

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Nature Communications, 2021
Nanopore sequencing technologies applied to transcriptome analysis suffer from high error rates, limiting them largely to reference-based analyses. Here, the authors develop a computational error correction method for transcriptome analysis that reduces ...
Kristoffer Sahlin, Botond Sipos, Phillip L. James, Paul Medvedev   +3 more
doaj   +1 more source

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

Genome Biology, 2021
We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing.
Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence Kwong, Phillip James, Daniel J. Turner, David Yu Zhang   +8 more
doaj   +1 more source

Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line

, 2022
One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at CpG dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many ...
Oxford Nanopore Technologies
core   +1 more source