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Journal articles on the topic 'MinION sequencing'

Author: Grafiati

Published: 11 March 2023

Last updated: 19 July 2025

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1

Batovska, Jana, Stacey E. Lynch, Brendan C. Rodoni, Tim I. Sawbridge, and Noel Oi Cogan. "Metagenomic arbovirus detection using MinION nanopore sequencing." Journal of Virological Methods 249 (June 12, 2017): 79–84. https://doi.org/10.5281/zenodo.13515287.

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(Uploaded by Plazi for the Bat Literature Project) With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample within a few hours. This study aimed to determine the ability of the MinION to metagenomically detect and characterise a virus from an infected mosquito. RNA was extracted from an Aedes notoscriptus mosquito infected with Ross River virus (RRV), converted into cDNA and sequenced on the MinION. Bioinformatic analysis of the MinION reads led to detecti

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Batovska, Jana, Stacey E. Lynch, Brendan C. Rodoni, Tim I. Sawbridge, and Noel Oi Cogan. "Metagenomic arbovirus detection using MinION nanopore sequencing." Journal of Virological Methods 249 (June 7, 2017): 79–84. https://doi.org/10.5281/zenodo.13515287.

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(Uploaded by Plazi for the Bat Literature Project) With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample within a few hours. This study aimed to determine the ability of the MinION to metagenomically detect and characterise a virus from an infected mosquito. RNA was extracted from an Aedes notoscriptus mosquito infected with Ross River virus (RRV), converted into cDNA and sequenced on the MinION. Bioinformatic analysis of the MinION reads led to detecti

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Batovska, Jana, Stacey E. Lynch, Brendan C. Rodoni, Tim I. Sawbridge, and Noel Oi Cogan. "Metagenomic arbovirus detection using MinION nanopore sequencing." Journal of Virological Methods 249 (July 3, 2017): 79–84. https://doi.org/10.5281/zenodo.13515287.

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(Uploaded by Plazi for the Bat Literature Project) With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample within a few hours. This study aimed to determine the ability of the MinION to metagenomically detect and characterise a virus from an infected mosquito. RNA was extracted from an Aedes notoscriptus mosquito infected with Ross River virus (RRV), converted into cDNA and sequenced on the MinION. Bioinformatic analysis of the MinION reads led to detecti

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Batovska, Jana, Stacey E. Lynch, Brendan C. Rodoni, Tim I. Sawbridge, and Noel Oi Cogan. "Metagenomic arbovirus detection using MinION nanopore sequencing." Journal of Virological Methods 249 (July 10, 2017): 79–84. https://doi.org/10.5281/zenodo.13515287.

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(Uploaded by Plazi for the Bat Literature Project) With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample within a few hours. This study aimed to determine the ability of the MinION to metagenomically detect and characterise a virus from an infected mosquito. RNA was extracted from an Aedes notoscriptus mosquito infected with Ross River virus (RRV), converted into cDNA and sequenced on the MinION. Bioinformatic analysis of the MinION reads led to detecti

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Lemon, Jamie K., Pavel P. Khil, Karen M. Frank, and John P. Dekker. "Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates." Journal of Clinical Microbiology 55, no. 12 (2017): 3530–43. http://dx.doi.org/10.1128/jcm.01069-17.

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ABSTRACTRecent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. In this study, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different li

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Agakhanov, M. M., E. A. Grigoreva, E. K. Potokina, P. S. Ulianich, and Y. V. Ukhatova. "Genome assembly of Vitis rotundifolia Michx. using third-generation sequencing (Oxford Nanopore Technologies)." Proceedings on applied botany, genetics and breeding 182, no. 2 (2021): 63–71. http://dx.doi.org/10.30901/2227-8834-2021-2-63-71.

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The immune North American grapevine species Vitis rotundifolia Michaux (subgen. Muscadinia Planch.) is regarded as a potential donor of disease resistance genes, withstanding such dangerous diseases of grapes as powdery and downy mildews. The cultivar ‘Dixie’ is the only representative of this species preserved ex situ in Russia: it is maintained by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in the orchards of its branch, Krymsk Experiment Breeding Station. Third-generation sequencing on the MinION platform was performed to obtain information on the primary structu

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Tafess, Ketema, Timothy Ting Leung Ng, Hiu Yin Lao, et al. "Targeted-Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis Cultures Using Two Commercial Sequencing Platforms: Comparison of Analytical and Diagnostic Performance, Turnaround Time, and Cost." Clinical Chemistry 66, no. 6 (2020): 809–20. http://dx.doi.org/10.1093/clinchem/hvaa092.

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Abstract Background The emergence of Mycobacterium tuberculosis with complex drug resistance profiles necessitates a rapid and comprehensive drug susceptibility test for guidance of patient treatment. We developed two targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the prediction of drug resistance in M. tuberculosis toward 12 antibiotics. Methods A total of 163 M. tuberculosis isolates collected from Hong Kong and Ethiopia were subjected to a multiplex PCR for simultaneous amplification of 19 drug resistance-associated genetic regions. The amplicons were then bar

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de Lannoy, Carlos, Dick de Ridder, and Judith Risse. "A sequencer coming of age: De novo genome assembly using MinION reads." F1000Research 6 (July 7, 2017): 1083. http://dx.doi.org/10.12688/f1000research.12012.1.

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Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new a

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de Lannoy, Carlos, Dick de Ridder, and Judith Risse. "The long reads ahead: de novo genome assembly using the MinION." F1000Research 6 (December 12, 2017): 1083. http://dx.doi.org/10.12688/f1000research.12012.2.

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Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new a

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Jaudou, Sandra, Mai-Lan Tran, Fabien Vorimore, Patrick Fach, and Sabine Delannoy. "Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli." PLOS ONE 17, no. 7 (2022): e0270751. http://dx.doi.org/10.1371/journal.pone.0270751.

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Next generation sequencing has become essential for pathogen characterization and typing. The most popular second generation sequencing technique produces data of high quality with very low error rates and high depths. One major drawback of this technique is the short reads. Indeed, short-read sequencing data of Shiga toxin-producing Escherichia coli (STEC) are difficult to assemble because of the presence of numerous mobile genetic elements (MGEs), which contain repeated elements. The resulting draft assemblies are often highly fragmented, which results in a loss of information, especially co

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Hosokawa-Muto, Junji, Yukiko Sassa-O’Brien, Yoshihito Fujinami, and Hiroaki Nakahara. "Analysis Comparison for Rapid Identification of Pathogenic Virus from Infected Tissue Samples." Diagnostics 12, no. 1 (2022): 196. http://dx.doi.org/10.3390/diagnostics12010196.

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When examining infectious samples, rapid identification of the pathogenic agent is required for diagnosis and treatment or for investigating the cause of death. In our previous study, we applied exhaustive amplification using non-specific primers (the rapid determination system of viral genome sequences, the RDV method) to identify the causative virus via swab samples from a cat with a suspected viral infection. The purpose of the current study is to investigate suitable methods for the rapid identification of causative pathogens from infected tissue samples. First, the influenza virus was ino

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Batovska, Jana, Stacey E. Lynch, Brendan C. Rodoni, Tim I. Sawbridge, and Noel OI Cogan. "Metagenomic arbovirus detection using MinION nanopore sequencing." Journal of Virological Methods 249 (November 2017): 79–84. http://dx.doi.org/10.1016/j.jviromet.2017.08.019.

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Lu, Hengyun, Francesca Giordano, and Zemin Ning. "Oxford Nanopore MinION Sequencing and Genome Assembly." Genomics, Proteomics & Bioinformatics 14, no. 5 (2016): 265–79. http://dx.doi.org/10.1016/j.gpb.2016.05.004.

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Ip, Camilla L. C., Matthew Loose, John R. Tyson, et al. "MinION Analysis and Reference Consortium: Phase 1 data release and analysis." F1000Research 4 (October 15, 2015): 1075. http://dx.doi.org/10.12688/f1000research.7201.1.

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The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global c

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Zhou, Yi. "From Sanger to Single Molecule: A Comparative Review of DNA Sequencing Technologies and Their Applications." Theoretical and Natural Science 99, no. 1 (2025): 102–8. https://doi.org/10.54254/2753-8818/2025.22532.

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This review provides a comprehensive overview of DNA sequencing technologies, including Sanger sequencing (the first generation), next-generation sequencing (NGS), and third-generation sequencing (TGS) such as SMRT and Oxford Nanopore MinION. Sanger sequencing, renowned for its high accuracy (up to 99.999% raw per-base accuracy), has limitations in parallel sample analysis, cost-effectiveness, and speed. As exemplified by Illumina's technology, NGS offers high throughput through in situ amplification on a solid surface but has shorter read lengths. TGS technologies like SMRT and Oxford Nanopor

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Werner, David, Kishor Acharya, Adrian Blackburn, et al. "MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research." Water 14, no. 16 (2022): 2491. http://dx.doi.org/10.3390/w14162491.

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In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items fo

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Hargreaves, Adam D., and John F. Mulley. "Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing." PeerJ 3 (November 24, 2015): e1441. http://dx.doi.org/10.7717/peerj.1441.

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Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper,Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% withde novoer

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Wei, Shan, Zachary R. Weiss, and Zev Williams. "Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform." G3: Genes|Genomes|Genetics 8, no. 5 (2018): 1649–57. http://dx.doi.org/10.1534/g3.118.200087.

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White, Ruby, Christophe Pellefigues, Franca Ronchese, Olivier Lamiable, and David Eccles. "Investigation of chimeric reads using the MinION." F1000Research 6 (May 5, 2017): 631. http://dx.doi.org/10.12688/f1000research.11547.1.

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Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A further investigation was carried out specifically to search for chimeric reads, using separate barcodes for each amplicon and trying two different ligation methods prior to sample loading. Despite the separation of ligation products, chimeric reads f

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White, Ruby, Christophe Pellefigues, Franca Ronchese, Olivier Lamiable, and David Eccles. "Investigation of chimeric reads using the MinION." F1000Research 6 (August 16, 2017): 631. http://dx.doi.org/10.12688/f1000research.11547.2.

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Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A further investigation was carried out specifically to search for chimeric reads, using separate barcodes for each amplicon and trying two different ligation methods prior to sample loading. Despite the separation of ligation products, chimeric reads f

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Seah, Adeline, Marisa C. W. Lim, Denise McAloose, Stefan Prost, and Tracie A. Seimon. "MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples." Genes 11, no. 4 (2020): 445. http://dx.doi.org/10.3390/genes11040445.

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The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinfo

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Lee, Yun Gyeong, Sang Chul Choi, Yuna Kang, Kyeong Min Kim, Chon-Sik Kang, and Changsoo Kim. "Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology." Plants 8, no. 8 (2019): 270. http://dx.doi.org/10.3390/plants8080270.

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The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the P

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Ostrovski, Hanna, Rodrigo Pelicioni Savegnago, Wen Huang, and Cedric Gondro. "PSXIV-24 Real-time, on-site whole genome sequencing with oxford nanopore technologies’ MinION." Journal of Animal Science 99, Supplement_3 (2021): 257–58. http://dx.doi.org/10.1093/jas/skab235.470.

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Abstract Most quantitative geneticists are traditionally trained for data analysis in genetic evaluation and genomic prediction, but rarely have extensive knowledge of molecular genetics or experience in experimental labs. Recent products, such as those launched by Oxford Nanopore Technologies (ONT), give those quantitative geneticists a comprehensible and hands-on toolkit to explore DNA sequencing. The ‘MinION’, a small DNA sequencer, is of interest for quantitative geneticists due to both the minimal learning curve and the non-proprietary USB connectivity. This device is small enough to be p

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Romero-Calle, Danitza Xiomara, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tomé, et al. "Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil." Microorganisms 11, no. 7 (2023): 1837. http://dx.doi.org/10.3390/microorganisms11071837.

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Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthro

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Kudjordjie, Enoch Narh, Anne Saaby Schmidt-Høier, Mai-Britt Brøndum, Mads Grønvald Johnsen, Mogens Nicolaisen, and Mette Vestergård. "Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing." PLOS ONE 19, no. 3 (2024): e0300381. http://dx.doi.org/10.1371/journal.pone.0300381.

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Water-borne plant pathogenic fungi and oomycetes are a major threat in greenhouse production systems. Early detection and quantification of these pathogens would enable us to ascertain both economic and biological thresholds required for a timely treatment, thus improving effective disease management. Here, we used Oxford nanopore MinION amplicon sequencing to analyze microbial communities in irrigation water collected from greenhouses used for growing tomato, cucumber and Aeschynanthus sp. Fungal and oomycete communities were characterized using primers that amplify the full internal transcri

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Bosch, Thijs, Rogier Schade, Fabian Landman, Leo Schouls, and Karin van Dijk. "A blaVIM-1 positive Aeromonas hydrophila strain in a near-drowning patient: evidence for interspecies plasmid transfer within the patient." Future Microbiology 14, no. 14 (2019): 1191–97. http://dx.doi.org/10.2217/fmb-2019-0091.

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Aim: To show that a strain of Aeromonas hydrophila became resistant to carbapenems by interspecies transfer of a plasmid using long-read sequencing. Material & methods: Whole genome sequencing of the four isolates was done using Illumina Hiseq, while the plasmid was reconstructed using the MinION sequencer. The resistome was identified with ResFinder. Results: Whole genome sequencing and long-read sequencing showed that all isolates carried a blaVIM-1 gene located on a 165 kb incA/C plasmid. ResFinder confirmed that the resistome of the plasmid, comprising 13 resistance genes, was identica

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Benítez-Páez, Alfonso, Kevin J. Portune, and Yolanda Sanz. "Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer." GigaScience 5, no. 1 (2016): 4. https://doi.org/10.1186/s13742-016-0111-z.

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<strong>Background: </strong>The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION™ system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.<strong>Results: </strong>Using R7.3 chemistry, we generated more than

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Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (August 24, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.2.

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Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through

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Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (May 12, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.1.

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Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through

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Wei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, et al. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform." International Journal of Molecular Sciences 21, no. 19 (2020): 7110. http://dx.doi.org/10.3390/ijms21197110.

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Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified

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Irinyi, Laszlo, Yiheng Hu, Minh Thuy Vi Hoang, et al. "Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics." Medical Mycology 58, no. 5 (2019): 650–60. http://dx.doi.org/10.1093/mmy/myz109.

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Abstract The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumo

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Garcia-Pedemonte, David, Albert Carcereny, Josep Gregori, et al. "Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater." International Journal of Molecular Sciences 24, no. 24 (2023): 17184. http://dx.doi.org/10.3390/ijms242417184.

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Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effe

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Baloğlu, Bilgenur, Zhewei Chen, Vasco Elbrecht, Thomas Braukmann, Shanna MacDonald, and Dirk Steinke. "A workflow for accurate metabarcoding using nanopore MinION sequencing." Methods in Ecology and Evolution 12, no. 5 (2021): 794–804. http://dx.doi.org/10.1111/2041-210x.13561.

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Preul, MarkC, Arpan Patel, Evgenii Belykh, et al. "MinION rapid sequencing: Review of potential applications in neurosurgery." Surgical Neurology International 9, no. 1 (2018): 157. http://dx.doi.org/10.4103/sni.sni_55_18.

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Rames, Emily, and Joanne Macdonald. "Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping." Virus Research 252 (July 2018): 8–12. http://dx.doi.org/10.1016/j.virusres.2018.05.010.

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Loman, Nick, Sarah Goodwin, Hans J. Jansen, and Matt Loose. "A disruptive sequencer meets disruptive publishing." F1000Research 4 (October 15, 2015): 1074. http://dx.doi.org/10.12688/f1000research.7229.1.

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Nanopore sequencing was recently made available to users in the form of the Oxford Nanopore MinION. Released to users through an early access programme, the MinION is made unique by its tiny form factor and ability to generate very long sequences from single DNA molecules. The platform is undergoing rapid evolution with three distinct nanopore types and five updates to library preparation chemistry in the last 18 months. To keep pace with the rapid evolution of this sequencing platform, and to provide a space where new analysis methods can be openly discussed, we present a new F1000Research ch

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Wallace, Amelia D., Thomas A. Sasani, Jordan Swanier, et al. "CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing." PLOS ONE 16, no. 4 (2021): e0241253. http://dx.doi.org/10.1371/journal.pone.0241253.

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A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequencing technologies, such as Oxford Nanopore’s MinION, enable direct measurement of complex loci without introducing many of the biases inherent to short-read methods, though they suffer from relatively lower throughput. This limitation has motivated recent efforts to develop amplification-free strategies to target and enrich loci of interest for subsequent sequencing with long reads. Here, we present

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Telussa, Rallya, Puji Rahayu, Thufeil Yunindika, et al. "Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers." Antibiotics 14, no. 7 (2025): 624. https://doi.org/10.3390/antibiotics14070624.

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Background: Antimicrobial resistance (AMR) poses significant risks to human and animal health, while the environment can contribute to its spread. National AMR surveillance programs are pivotal for assessing AMR prevalence, trends, and intervention outcomes; however, integrating advanced surveillance tools can be difficult. This pilot study, conducted by FAO ECTAD Indonesia and DGLAHS, the Indonesian Ministry of Agriculture, evaluated the costs and benefits of integrating the Nanopore MinION, Illumina MiSeq, and Sensititre system into a culture-based slaughterhouse–river surveillance system. M

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Crossley, Beate M., Daniel Rejmanek, John Baroch, et al. "Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses." Journal of Veterinary Diagnostic Investigation 33, no. 2 (2021): 253–60. http://dx.doi.org/10.1177/1040638720984114.

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We report whole-genome sequencing of influenza A virus (IAV) with 100% diagnostic sensitivity and results available in <24–48 h using amplicon-based nanopore sequencing technology (MinION) on clinical material from wild waterfowl ( n = 19), commercial poultry ( n = 4), and swine ( n = 3). All 8 gene segments of IAV including those from 14 of the 18 recognized hemagglutinin subtypes and 9 of the 11 neuraminidase subtypes were amplified in their entirety at >500× coverage from each of 16 reference virus isolates evaluated. Subgenomic viral sequences obtained in 3 cases using Sanger sequenc

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Schuele, Leonard, Hayley Cassidy, Erley Lizarazo, et al. "Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples." Viruses 12, no. 12 (2020): 1358. http://dx.doi.org/10.3390/v12121358.

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Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the vi

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Leggett, Richard M., Cristina Alcon-Giner, Darren Heavens, et al. "Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens." Nature Microbiology 5, no. 3 (2019): 430–42. http://dx.doi.org/10.1038/s41564-019-0626-z.

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AbstractThe MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or ep

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Kask, Oliver, Mark Knappenberger, Heewook Lee, Alicia Van Stone, and Karen Anderson. "HLA-PopSeq: High throughput, multiplexed six-locus Human Leukocyte Antigen typing for population-scale T cell immune profiling using rapid long-read nanopore sequencing." Journal of Immunology 210, no. 1_Supplement (2023): 250.10. http://dx.doi.org/10.4049/jimmunol.210.supp.250.10.

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Abstract A major technical hurdle for T cell immune profiling is the time and cost to accurately genotype the Human Leukocyte Antigen (HLA) loci from peripheral blood. Here, we developed a rapid, highly multiplexed approach for HLA typing using RNA from &lt;100,000 peripheral blood mononuclear cells with the Oxford Nanopore Technology (ONT) Minion sequencer. This method uses selective reverse transcription of mRNA of six HLA loci (A,B,C, DRB1, DQB1, DPB1), followed by PCR amplification. The individual amplified HLA cDNA was multiplexed in a single sequencing pool using primers with unique

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Boutigny, Anne-Laure, Florent Fioriti, and Mathieu Rolland. "Targeted MinION sequencing of transgenes." Scientific Reports 10, no. 1 (2020). http://dx.doi.org/10.1038/s41598-020-71614-6.

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Abstract The presence of genetically modified organisms (GMO) is commonly assessed using real-time PCR methods targeting the most common transgenic elements found in GMOs. Once the presence of GM material has been established using these screening methods, GMOs are further identified using a battery of real-time PCR methods, each being specific of one GM event and usually targeting the junction of the plant genome and of the transgenic DNA insert. If, using these specific methods, no GMO could be identified, the presence of an unauthorized GMO is suspected. In this context, the aim of this wor

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Pecman, Anja, Ian Adams, Ion Gutiérrez-Aguirre, et al. "Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach." Frontiers in Microbiology 13 (May 11, 2022). http://dx.doi.org/10.3389/fmicb.2022.883921.

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High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology

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Cabibbe, Andrea M., Andrea Spitaleri, Simone Battaglia, et al. "Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples." Journal of Clinical Microbiology 58, no. 10 (2020). http://dx.doi.org/10.1128/jcm.00632-20.

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ABSTRACT Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted fro

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Miura, Hiroto, Masayuki Takeda, Megumi Yamaguchi, et al. "Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis." Frontiers in Microbiology 13 (March 24, 2022). http://dx.doi.org/10.3389/fmicb.2022.783058.

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The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated

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Phillips, Laura T., Adam A. Witney, Martina Furegato, Ken G. Laing, Liqing Zhou, and S. Tariq Sadiq. "Time required for nanopore whole genome sequencing of Neisseria gonorrhoeae for identification of phylogenetic relationships." Journal of Infectious Diseases, May 22, 2023. http://dx.doi.org/10.1093/infdis/jiad170.

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Abstract Background Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health challenge. Limitations to AMR surveillance reporting, alongside reduction in culture-based susceptibility testing, has resulted in a need for rapid diagnostics and strain detection. We investigated Nanopore sequencing time, and depth, to accurately identify closely related N. gonorrhoeae isolates, compared to Illumina sequencing. Methods N. gonorrhoeae strains collected from a London Sexual Health clinic were cultured and sequenced with MiSeq and MinION sequencing platforms. Accuracy was determined b

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Mariner-Llicer, Carla, Galo A. Goig, Laura Zaragoza-Infante, et al. "Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes." Microbial Genomics 7, no. 12 (2021). http://dx.doi.org/10.1099/mgen.0.000740.

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A rapid and accurate diagnostic assay represents an important means to detect Mycobacterium tuberculosis , identify drug-resistant strains and ensure treatment success. Currently employed techniques to diagnose drug-resistant tuberculosis include slow phenotypic tests or more rapid molecular assays that evaluate a limited range of drugs. Whole-genome-sequencing-based approaches can detect known drug-resistance-conferring mutations and novel variations; however, the dependence on growing samples in culture, and the associated delays in achieving results, represents a significant limitation. As

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McHugh, Aoife J., Min Yap, Fiona Crispie, Conor Feehily, Colin Hill, and Paul D. Cotter. "Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples." npj Science of Food 5, no. 1 (2021). http://dx.doi.org/10.1038/s41538-021-00087-2.

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AbstractEfficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to

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Hikida, Hiroyuki, Yusuke Okazaki, Ruixuan Zhang, Thi Tuyen Nguyen, and Hiroyuki Ogata. "A rapid genome‐wide analysis of isolated giant viruses using MinION sequencing." Environmental Microbiology, August 5, 2023. http://dx.doi.org/10.1111/1462-2920.16476.

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AbstractFollowing the discovery of Acanthamoeba polyphaga mimivirus, diverse giant viruses have been isolated. However, only a small fraction of these isolates have been completely sequenced, limiting our understanding of the genomic diversity of giant viruses. MinION is a portable and low‐cost long‐read sequencer that can be readily used in a laboratory. Although MinION provides highly error‐prone reads that require correction through additional short‐read sequencing, recent studies assembled high‐quality microbial genomes only using MinION sequencing. Here, we evaluated the accuracy of MinIO

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