Nanocall: an open source basecaller for Oxford Nanopore sequencing data [PDF]
Bioinformatics, 2017 MotivationThe highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally
Simpson, Jared T +4 more
core +6 more sources
Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies [PDF]
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 +11 more
doaj +2 more sources
NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing [PDF]
Bioinformatics, 2022 MOTIVATION: Long-read sequencing methods have considerable advantages for characterizing RNA isoforms. Oxford Nanopore sequencing records changes in electrical current when nucleic acid traverses through a pore.
Clark, Michael B +5 more
core +4 more sources
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling [PDF]
BioinformaticsThe data underlying this article will be shared on reasonable request to the corresponding author.[Motivation]: Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run.
Munro, Rory +4 more
core +4 more sources
A comparison of Oxford nanopore library strategies for bacterial genomics [PDF]
BMC Genomics, 2023 Abstract Background Oxford nanopore Technologies (ONT) provides three main library preparation strategies to sequence bacterial genomes. These include tagmentation (TAG), ligation (LIG) and amplification (PCR). Despite ONT’s recommendations, making an informed decision for preparation choice remains difficult without a ...
Sauvage, Thomas +2 more
openaire +3 more sources
Optimized use of Oxford Nanopore flowcells for hybrid assemblies [PDF]
Microbial Genomics, 2020 Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the ...
Samuel Lipworth +14 more
openaire +3 more sources
Application of Oxford Nanopore Technology to Plant Virus Detection [PDF]
Viruses, 2021 The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification.
Lia W. Liefting +2 more
openaire +3 more sources
Prowler: A novel trimming algorithm for Oxford Nanopore sequence data [PDF]
Bioinformatics, 2021 Abstract Motivation Quality control (QC) tools are critical in DNA sequencing analysis because they increase the accuracy of sequence alignments and thus the reliability of results. Oxford Nanopore Technologies (ONT) QC is currently rudimentary, generally based on whole read average quality.
Simon Lee +3 more
openaire +5 more sources
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
Assessing FOXA1-driven mRNA processing in prostate cancer with Nanopore long-read sequencing
, 2022 Despite advances in the diagnosis and treatment of early stage of prostate cancer (PC), there are few therapeutic options for end-stage metastatic castration-resistant PC.
Matteo Cereda
core +2 more sources