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Journal articles on the topic 'Oxford Nanopore sequencing'

Author: Grafiati

Published: 14 March 2023

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1

Heikema, Astrid P., Deborah Horst-Kreft, Stefan A. Boers, et al. "Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota." Genes 11, no. 9 (2020): 1105. http://dx.doi.org/10.3390/genes11091105.

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Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequenci

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Lin, Bo, Jianan Hui, and Hongju Mao. "Nanopore Technology and Its Applications in Gene Sequencing." Biosensors 11, no. 7 (2021): 214. http://dx.doi.org/10.3390/bios11070214.

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In recent years, nanopore technology has become increasingly important in the field of life science and biomedical research. By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules. One of the most successful applications of nanopore technology, the Oxford Nanopore Technology, marks the beginning of the fourth generation of gene sequencing technology. In this review, the operational principle and the technology for signal processing of the nanopore gene sequencing ar

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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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4

Eisenstein, Michael. "Oxford Nanopore announcement sets sequencing sector abuzz." Nature Biotechnology 30, no. 4 (2012): 295–96. http://dx.doi.org/10.1038/nbt0412-295.

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Sereika, Mantas, Rasmus Hansen Kirkegaard, Søren Michael Karst, et al. "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 19, no. 7 (2022): 823–26. http://dx.doi.org/10.1038/s41592-022-01539-7.

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AbstractLong-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.

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MacKenzie, Morgan, and Christos Argyropoulos. "An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations." Micromachines 14, no. 2 (2023): 459. http://dx.doi.org/10.3390/mi14020459.

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There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understandin

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Салахов, Р. Р., М. В. Голубенко, Е. Н. Павлюкова, et al. "Application of monomolecular sequencing technology to the diagnostics of hypertrophic cardiomyopathy." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 5(214) (May 29, 2020): 9–10. http://dx.doi.org/10.25557/2073-7998.2020.05.9-10.

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В работе представлены результаты секвенирования пяти генов, ассоциированных с гипертрофической кардиомиопатией, с использованием технологии мономолекулярного секвенирования компании Oxford Nanopore Technologies. В результате анализа данных с помощью различных алгоритмов были выявлены миссенс-варианты в исследованных генах, которые могут являться причиной заболевания у пациентов. The paper presents the results of sequencing of five genes associated with hypertrophic cardiomyopathy, using monomolecular sequencing (Oxford Nanopore Technologies). As a result of data analysis with various algorithm

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Burns, Adam, David Robert Bruce, Pauline Robbe, et al. "Detection of Clinically Relevant Molecular Alterations in Chronic Lymphocytic Leukemia (CLL) By Nanopore Sequencing." Blood 132, Supplement 1 (2018): 1847. http://dx.doi.org/10.1182/blood-2018-99-110948.

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Abstract Introduction Chronic Lymphocytic Leukaemia (CLL) is the most prevalent leukaemia in the Western world and characterised by clinical heterogeneity. IgHV mutation status, mutations in the TP53 gene and deletions of the p-arm of chromosome 17 are currently used to predict an individual patient's response to therapy and give an indication as to their long-term prognosis. Current clinical guidelines recommend screening patients prior to initial, and any subsequent, treatment. Routine clinical laboratory practices for CLL involve three separate assays, each of which are time-consuming and r

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Dumschott, Kathryn, Maximilian H.-W. Schmidt, Harmeet Singh Chawla, Rod Snowdon, and Björn Usadel. "Oxford Nanopore sequencing: new opportunities for plant genomics?" Journal of Experimental Botany 71, no. 18 (2020): 5313–22. http://dx.doi.org/10.1093/jxb/eraa263.

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Abstract DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especiall

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Leger, Adrien, and Tommaso Leonardi. "pycoQC, interactive quality control for Oxford Nanopore Sequencing." Journal of Open Source Software 4, no. 34 (2019): 1236. http://dx.doi.org/10.21105/joss.01236.

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Chen, Weigang, Peng Zhang, Lifu Song, Jinsheng Yang, and Changcai Han. "Simulation of Nanopore Sequencing Signals Based on BiGRU." Sensors 20, no. 24 (2020): 7244. http://dx.doi.org/10.3390/s20247244.

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Oxford Nanopore sequencing is an important sequencing technology, which reads the nucleotide sequence by detecting the electrical current signal changes when DNA molecule is forced to pass through a biological nanopore. The research on signal simulation of nanopore sequencing is highly desirable for method developments of nanopore sequencing applications. To improve the simulation accuracy, we propose a novel signal simulation method based on Bi-directional Gated Recurrent Units (BiGRU). In this method, the signal processing model based on BiGRU is built to replace the traditional low-pass fil

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Czmil, Anna, Michal Wronski, Sylwester Czmil, et al. "NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology." PeerJ 10 (March 29, 2022): e13056. http://dx.doi.org/10.7717/peerj.13056.

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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 biologists, medics and geneticists across various applications. Oxford Nanopore is automated and relatively simple for conducting experiments, but generates gigabytes of raw data, to be processed by often ambiguous set of alternative bioinformatics command-line tools, and genomics frameworks which require a knowledge of bioinformatics to run. Results W

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Lamb, Harrison J., Ben J. Hayes, Loan T. Nguyen, and Elizabeth M. Ross. "The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock." Genes 11, no. 12 (2020): 1478. http://dx.doi.org/10.3390/genes11121478.

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Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and

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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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Zhao, Kaishun, Chunlin Tu, Wei Chen, et al. "Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing." Canadian Journal of Infectious Diseases and Medical Microbiology 2022 (March 28, 2022): 1–8. http://dx.doi.org/10.1155/2022/7588033.

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Mycobacterium tuberculosis antimicrobial resistance has been continually reported and is a major public health issue worldwide. Rapid prediction of drug resistance is important for selecting appropriate antibiotic treatments, which significantly increases cure rates. Gene sequencing technology has proven to be a powerful strategy for identifying relevant drug resistance information. This study established a sequencing method and bioinformatics pipeline for resistance gene analysis using an Oxford Nanopore Technologies sequencer. The pipeline was validated by Sanger sequencing and exhibited 100

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Tytgat, Olivier, Yannick Gansemans, Jana Weymaere, Kaat Rubben, Dieter Deforce, and Filip Van Nieuwerburgh. "Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling." Genes 11, no. 4 (2020): 381. http://dx.doi.org/10.3390/genes11040381.

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Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The goal of this study was to apply the latest progress in nanopore sequencing by Oxford Nanopore Technologies in the field of STR genotyping. The experiments were performed using the state of the art R9.4 flow cell and the most recent R10 flow cell, which was specifically designed to improve consensus accura

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Kinimi, Edson, Mana Mahapatra, Tebogo Kgotlele, et al. "Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses." Animals 11, no. 10 (2021): 2976. http://dx.doi.org/10.3390/ani11102976.

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Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic surveillance tools is critical where PPR is endemic. Genomic data can provide sufficient in-depth information to identify the pockets of endemicity responsible for PPRV persistence and viral evolution, and direct an appropriate vaccination response. Yet, access to the required sequencing technology

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Chen, Zhao, David L. Erickson, and Jianghong Meng. "Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing." International Journal of Molecular Sciences 21, no. 23 (2020): 9161. http://dx.doi.org/10.3390/ijms21239161.

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Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested

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Liem, Michael, Hans J. Jansen, Ron P. Dirks, et al. "De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing." F1000Research 6 (August 3, 2018): 618. http://dx.doi.org/10.12688/f1000research.11146.2.

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Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful for accurate annotation of all genes in the genome. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequencing protocol, showing that

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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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Diubo, Yulia V., Artur E. Akhremchuk, Leonid N. Valentovich, and Yevgeny A. Nikolaichik. "Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A." Journal of the Belarusian State University. Biology, no. 3 (November 4, 2021): 71–77. http://dx.doi.org/10.33581/2521-1722-2021-3-71-77.

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The methylation profile of Pectobacterium carotovorum 2A genome was studied using the Oxford Nanopore sequencing technology. The specificity of the methylase subunits of the three restriction-modification systems of this strain was determined. Analysis of homologous systems showed the uniqueness of the type I restriction-modification system and the type IV restriction system specific to methylated DNA of this strain. The work confirms the applicability of Oxford Nanopore technology to the analysis of bacterial DNA modifications and is also the first example of such an analysis for Pectobacteri

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Du, Chenghao. "The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19." E3S Web of Conferences 271 (2021): 04024. http://dx.doi.org/10.1051/e3sconf/202127104024.

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The novel coronavirus disease 2019 (COVID‐19), originally identified in December 2019 Wuhan, China, has propagated to worldwide pandemic, causing many cases of death and morbidity. Since the development of COVID-19 vaccines is still under experimental stages without public access, different types of testing and detection ensuring rapid and accurate results are urgently required to prevent delaying isolation of infected patients. The traditional diagnostic and analytical methods of COVID-19 relied heavily on nucleic acid and antibody-antigen methods but are subject to assembly bias, restricted

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Du, Chenghao. "The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19." South Florida Journal of Development 2, no. 3 (2021): 4014–28. http://dx.doi.org/10.46932/sfjdv2n3-017.

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The novel coronavirus disease 2019 (COVID‐19), originally identified in December 2019 Wuhan, China, has propagated to worldwide pandemic, causing many cases of death and morbidity. Since the development of COVID-19 vaccines is still under experimental stages without public access, different types of testing and detection ensuring rapid and accurate results are urgently required to prevent delaying isolation of infected patients. The traditional diagnostic and analytical methods of COVID-19 relied heavily on nucleic acid and antibody-antigen methods but are subject to assembly bias, restricted

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Deynichenko, K. A., K. G. Ptitsyn, S. P. Radko, et al. "Splice variants of mRNA of cytochrome P450 genes: analysis by the nanopore sequencing method in human liver tissue and HepG2 cell line." Biomeditsinskaya Khimiya 68, no. 2 (2022): 117–25. http://dx.doi.org/10.18097/pbmc20226802117.

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The analysis of cytochrome P450 transcripts was carried out by the nanopore sequencing in liver tissue samples of three donors and HepG2 line cells. It has been demonstrated that direct mRNA sequencing with a MinION nanopore sequencer (Oxford Nanopore Technologies) allows one to obtained quantitative profiles for transcripts (and their splice variants) of cytochrome P450 superfamily genes encoding isoforms involved in metabolism of the large (~80%) part of drugs. The splice variant profiles substantially differ for donors. The cytochrome P450 gene expression at the transcript level is signific

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Tanaka, Mami, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, and Tomoo Sawabe. "Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case." PeerJ 6 (June 18, 2018): e5018. http://dx.doi.org/10.7717/peerj.5018.

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Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivo

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Radko, S. P., L. K. Kurbatov, K. G. Ptitsyn, et al. "Prospects for the use of third generation sequencers for quantitative profiling of transcriptome." Biomedical Chemistry: Research and Methods 1, no. 4 (2018): e00086. http://dx.doi.org/10.18097/bmcrm00086.

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Transcriptome profiling is widely employed to analyze transcriptome dynamics when studying various biological processes at the cell and tissue levels. Unlike the second generation sequencers, which sequence relatively short fragments of nucleic acids, the third generation DNA/RNA sequencers developed by biotechnology companies “PacBio” and “Oxford Nanopore Technologies” allow one to sequence transcripts as single molecules and may be considered as potential molecular counters capable to measure the number of copies of each transcript with high throughput, sensitivity, and specificity. In the p

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De Coster, Wouter, Endre Bakken Stovner, and Mojca Strazisar. "Methplotlib: analysis of modified nucleotides from nanopore sequencing." Bioinformatics 36, no. 10 (2020): 3236–38. http://dx.doi.org/10.1093/bioinformatics/btaa093.

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Abstract Summary Modified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele-specific modification within-subjects and differential modification frequency across subjects. Availability and implementation The methplotlib command-line tool is written in Python3, is compatible with Linux, Mac OS and the MS Windows 10 Subsystem for Linux and released under the MI

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Il Jun, Kang, Jangsup Moon, Taek Soo Kim, et al. "238. Direct identification of Bacterial Species with MinION Nanopore Sequencer In Clinical Specimens Suspected of Polybacterial Infection." Open Forum Infectious Diseases 6, Supplement_2 (2019): S136. http://dx.doi.org/10.1093/ofid/ofz360.313.

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Abstract Background Conventional culture tests usually identify only a few bacterial species, which can grow well in the culture system, in the cases of polybacterial infection. 16S rRNA gene nanopore sequencing enables semi-quantitative identification of bacterial genetic materials. We aimed to evaluate usefulness of 16s rRNA gene nanopore sequencing in the cases suspected of polybacterial infection. Methods The research was conducted in a single university hospital for one year. Conventional bacterial culture identification and nanopore sequencing of 16s rRNA gene were carried out simultaneo

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Jansen, Hans J., Ron P. Dirks, Michael Liem, et al. "De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing." F1000Research 6 (May 3, 2017): 618. http://dx.doi.org/10.12688/f1000research.11146.1.

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Background: The introduction of the MinIONTM sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. It has been shown that the nanopore sequence data, in combination with other sequencing technologies, is highly useful for accurate annotation of all genes in the genome. However, it also offers great potential for de novo assembly of complex genomes without using other technologies. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequen

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Morsli, Madjid, Quentin Kerharo, Jeremy Delerce, Pierre-Hugues Roche, Lucas Troude, and Michel Drancourt. "Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report." Pathogens 10, no. 4 (2021): 461. http://dx.doi.org/10.3390/pathogens10040461.

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Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding

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David, Matei, L. J. Dursi, Delia Yao, Paul C. Boutros, and Jared T. Simpson. "Nanocall: an open source basecaller for Oxford Nanopore sequencing data." Bioinformatics 33, no. 1 (2016): 49–55. http://dx.doi.org/10.1093/bioinformatics/btw569.

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Ding, Hongxu, Andrew D. Bailey, Miten Jain, Hugh Olsen, and Benedict Paten. "Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts." Bioinformatics 36, no. 19 (2020): 4928–34. http://dx.doi.org/10.1093/bioinformatics/btaa601.

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Abstract Motivation Nucleotide modification status can be decoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current signals. Although various algorithms have been developed for nanopore-sequencing-based modification analysis, more detailed characterizations, such as modification numbers, corresponding signal levels and proportions are still lacking. Results We present a framework for the unsupervised determination of the number of nucleotide modifications from nanopore-sequencing readouts. We demonstrate the approach can effectively recapitulate the number of modification

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Salakhov, R. R., M. V. Golubenko, E. N. Pavlukova, et al. "Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing." Russian Journal of Cardiology 26, no. 10 (2021): 4673. http://dx.doi.org/10.15829/1560-4071-2021-4673.

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Aim. To investigate the application of the Oxford Nanopore Technologies’ third generation sequencing for the genetic testing of hypertrophic cardiomyopathy.Material and methods. The study involved 12 patients with hypertrophic cardiomyopathy aged 18 to 67 years (women, 9; men, 3). Using the PCR barcoding amplicons (SQK-LSK109) protocol, DNA libraries were created which contained long-range PCR fragments of the MYH7, MYBPC3, TNNT2, TNNI3 and TPM1 genes. The sequencing was performed using the MinION system by Oxford Nanopore Technologies (UK). Bioinformatic algorithms for data analysis included

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Fukasawa, Yoshinori, Luca Ermini, Hai Wang, Karen Carty, and Min-Sin Cheung. "LongQC: A Quality Control Tool for Third Generation Sequencing Long Read Data." G3: Genes|Genomes|Genetics 10, no. 4 (2020): 1193–96. http://dx.doi.org/10.1534/g3.119.400864.

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We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key statistics were optimized for long read data, and LongQC covers all major TGS platforms. LongQC processes and visualizes those statistics automatically and quickly.

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Noone, J. Christopher, Karin Helmersen, Truls Michael Leegaard, Inge Skråmm, and Hege Vangstein Aamot. "Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies." Microorganisms 9, no. 1 (2021): 97. http://dx.doi.org/10.3390/microorganisms9010097.

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Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic

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Chen, Zhiao, and Xianghuo He. "Application of third-generation sequencing in cancer research." Medical Review 1, no. 2 (2021): 150–71. http://dx.doi.org/10.1515/mr-2021-0013.

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Abstract In the past several years, nanopore sequencing technology from Oxford Nanopore Technologies (ONT) and single-molecule real-time (SMRT) sequencing technology from Pacific BioSciences (PacBio) have become available to researchers and are currently being tested for cancer research. These methods offer many advantages over most widely used high-throughput short-read sequencing approaches and allow the comprehensive analysis of transcriptomes by identifying full-length splice isoforms and several other posttranscriptional events. In addition, these platforms enable structural variation cha

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Istace, Benjamin, Caroline Belser, Cyril Falentin, et al. "Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case." Biology 10, no. 8 (2021): 732. http://dx.doi.org/10.3390/biology10080732.

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With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv.

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de Siqueira, Guilherme Marcelino Viana, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, and María-Eugenia Guazzaroni. "Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units." Frontiers in Public Health 9 (August 27, 2021). http://dx.doi.org/10.3389/fpubh.2021.710985.

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Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively valid

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Neumann, Don, Anireddy S. N. Reddy, and Asa Ben-Hur. "RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data." BMC Bioinformatics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12859-022-04686-y.

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Abstract Background Despite recent progress in basecalling of Oxford nanopore DNA sequencing data, its wide adoption is still being hampered by its relatively low accuracy compared to short read technologies. Furthermore, very little of the recent research was focused on basecalling of RNA data, which has different characteristics than its DNA counterpart. Results We fill this gap by benchmarking a fully convolutional deep learning basecalling architecture with improved performance compared to Oxford nanopore’s RNA basecallers. Availability The source code for our basecaller is available at: h

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Silvestre-Ryan, Jordi, and Ian Holmes. "Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing." Genome Biology 22, no. 1 (2021). http://dx.doi.org/10.1186/s13059-020-02255-1.

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AbstractWe develop a general computational approach for improving the accuracy of basecalling with Oxford Nanopore’s 1D2 and related sequencing protocols. Our software PoreOver (https://github.com/jordisr/poreover) finds the consensus of two neural networks by aligning their probability profiles, and is compatible with multiple nanopore basecallers. When applied to the recently-released Bonito basecaller, our method reduces the median sequencing error by more than half.

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Qi, Weihong, Andrea Colarusso, Miriam Olombrada, et al. "New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies." Scientific Reports 9, no. 1 (2019). http://dx.doi.org/10.1038/s41598-019-52832-z.

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Abstract Pseudoalteromonas haloplanktis TAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance, P. haloplanktis has a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and dra

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Sun, Kai, Yi Liu, Xin Zhou, et al. "Nanopore sequencing technology and its application in plant virus diagnostics." Frontiers in Microbiology 13 (July 25, 2022). http://dx.doi.org/10.3389/fmicb.2022.939666.

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Plant viruses threaten crop yield and quality; thus, efficient and accurate pathogen diagnostics are critical for crop disease management and control. Recent advances in sequencing technology have revolutionized plant virus research. Metagenomics sequencing technology, represented by next-generation sequencing (NGS), has greatly enhanced the development of virus diagnostics research because of its high sensitivity, high throughput and non-sequence dependence. However, NGS-based virus identification protocols are limited by their high cost, labor intensiveness, and bulky equipment. In recent ye

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Liu, Yang, Wojciech Rosikiewicz, Ziwei Pan, et al. "DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation." Genome Biology 22, no. 1 (2021). http://dx.doi.org/10.1186/s13059-021-02510-z.

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Abstract Background Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies. Results We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale.

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Riaz, Nasir, Preston Leung, Kirston Barton, et al. "Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07460-1.

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Abstract Background Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. With the advent of third generation long read sequencing technologies, including Oxford Nanopore Technology (ONT) and PacBio pl

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Kerkhof, Lee J. "Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?" FEMS Microbiology Ecology 97, no. 3 (2021). http://dx.doi.org/10.1093/femsec/fiab001.

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ABSTRACT This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment a

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Goodwin, Sara, Robert Wappel, and W. Richard McCombie. "1D Genome Sequencing on the Oxford Nanopore MinION." Current Protocols in Human Genetics 94, no. 1 (2017). http://dx.doi.org/10.1002/cphg.39.

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Jain, Miten, Hugh E. Olsen, Benedict Paten, and Mark Akeson. "The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community." Genome Biology 17, no. 1 (2016). http://dx.doi.org/10.1186/s13059-016-1103-0.

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Sultan, Madiha, and Anastassia Kanavarioti. "Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag." Scientific Reports 9, no. 1 (2019). http://dx.doi.org/10.1038/s41598-019-50459-8.

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Abstract Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2′-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos a

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Prall, Trent M., Emma K. Neumann, Julie A. Karl, et al. "Consistent ultra-long DNA sequencing with automated slow pipetting." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07500-w.

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Abstract Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules through library preparation by pipetting reagents as slowly as possible to minimize shearing. This process is time-consuming and inconsistent at preserving read length as even small changes in volumetric flow rate can result in template shearing. Results We have designed SNAILS (Slow Nucleic Acid Instrume

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