Journal articles: 'Minion'

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Rusk, Nicole. "MinION takes center stage." Nature Methods 12, no. 1 (December 30, 2014): 12. http://dx.doi.org/10.1038/nmeth.3244.

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Rowan, Chris. "Meet my lab minion." Nature 450, no. 7167 (November 2007): 316. http://dx.doi.org/10.1038/nj7167-316c.

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Andracki, Thaddeus. "Minion by John David Anderson." Bulletin of the Center for Children's Books 68, no. 1 (2014): 5. http://dx.doi.org/10.1353/bcc.2014.0706.

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Minion, F. ,. Chris. "Molecular pathogenesis of mycoplasma animal respiratory pathogens." Frontiers in Bioscience 7, no. 1-3 (2002): d1410. http://dx.doi.org/10.2741/minion.

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Tafess, Ketema, Timothy Ting Leung Ng, Hiu Yin Lao, Kenneth Siu Sing Leung, Kingsley King Gee Tam, Rahim Rajwani, Sarah Tsz Yan Tam, 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 (May 2, 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 barcoded and sequenced in parallel on MiSeq and MinION in respective batch sizes of 24 and 12 samples. A web-based bioinformatics pipeline, BacterioChek-TB, was developed to translate the raw datasets into clinician-friendly reports. Results Both platforms successfully sequenced all samples with mean read depths of 1,127× and 1,649×, respectively. The variant calling by MiSeq and MinION could achieve 100% agreement if variants with an allele frequency of <40% reported by MinION were excluded. Both workflows achieved a mean clinical sensitivity of 94.8% and clinical specificity of 98.0% when compared with phenotypic drug susceptibility test (pDST). Turnaround times for the MiSeq and MinION workflows were 38 and 15 h, facilitating the delivery of treatment guidance at least 17–18 days earlier than pDST, respectively. The higher cost per sample on the MinION platform ($71.56) versus the MiSeq platform ($67.83) was attributed to differences in batching capabilities. Conclusion Our study demonstrates the interchangeability of MiSeq and MinION platforms for generation of accurate and actionable results for the treatment of tuberculosis.

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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 (July 1, 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 structure of the cultivar’s genomic DNA, employing also the results of Illumina sequencing available in databases. A detailed description of the technique with modifications at various stages is presented, as it was used for grapevine genome sequencing and whole-genome sequence assembly. The modified technique included the main stages of the original protocol recommended by the MinION producer: 1) DNA extraction; 2) preparation of libraries for sequencing; 3) MinION sequencing and bioinformatic data processing; 4) de novo whole-genome sequence assembly using only MinION data or hybrid assembly (MinION+Illumina data); and 5) functional annotation of the whole-genome assembly. Stage 4 included not only de novo sequencing, but also the analysis of the available bioinformatic data, thus minimizing errors and increasing precision during the assembly of the studied genome. The DNA isolated from the leaves of cv. ‘Dixie’ was sequenced using two MinION flow cells (R9.4.1).

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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 (October 11, 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 library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection. We specifically evaluated the advantages of using plasmid DNA for sequencing and the value of supplementing MinION sequences with MiSeq reads for increasing assembly accuracy. Resequencing of three plasmids in a referenceKlebsiella pneumoniaeisolate demonstrated ∼99% accuracy of draft MinION-only assembly and >99.9% accuracy of assembly polished with MiSeq reads. Plasmid DNA sequencing of previously uncharacterized clinical extended-spectrum β-lactamase (ESBL)-producingEscherichia coliandK. pneumoniaeisolates using MinION allowed successful identification of antimicrobial resistance genes in the draft assembly corresponding to all classes of observed plasmid-based phenotypic resistance. Importantly, use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing. With a MinION-only workflow that balances accuracy against turnaround time, full annotation of plasmid resistance gene content could be obtained in under 6 h from a subcultured isolate, less time than traditional phenotypic susceptibility testing.

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Sinha, Gunjan. "A New King and His Tiny Minion." Scientific American 275, no. 2 (August 1996): 24. http://dx.doi.org/10.1038/scientificamerican0896-24b.

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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 formed from different amplicons were still observed in the base-called sequence.The long-read nature of nanopore sequencing presents an effective tool for the discovery and filtering of chimeric reads. We have found that at least 1.7% of reads prepared using the Nanopore LSK002 2D Ligation Kit include post-amplification chimeric elements. This finding has potential implications for other amplicon sequencing technologies, as the process is unlikely to be specific to the sample preparation used for nanopore sequencing.

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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 formed from different amplicons were still observed in the base-called sequence. The long-read nature of nanopore sequencing presents an effective tool for the discovery and filtering of chimeric reads. We have found that at least 1.7% of reads prepared using the Nanopore LSK002 2D Ligation Kit include post-amplification chimeric elements. This finding has potential implications for other amplicon sequencing technologies, as the process is unlikely to be specific to the sample preparation used for nanopore sequencing.

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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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Bouche, Thierry. "Minion MM : installer une famille de fontes." Cahiers GUTenberg, no. 26 (1997): 45–70. http://dx.doi.org/10.5802/cg.208.

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Bingeman, John M. "Yarmouth Roads Wreck-Site-Alberghetti Bronze Minion." International Journal of Nautical Archaeology 38, no. 1 (March 2009): 173. http://dx.doi.org/10.1111/j.1095-9270.2008.00219.x.

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

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Białasek, Maciej, and Aleksandra Miłobędzka. "Revealing antimicrobial resistance in stormwater with MinION." Chemosphere 258 (November 2020): 127392. http://dx.doi.org/10.1016/j.chemosphere.2020.127392.

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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 assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of oversight in the expanding landscape of analysis tools, as performance evaluations are outdated quickly. Now that the MinION is approaching a state of maturity, a thorough comparative benchmarking effort of de novo assembly pipelines may be at place. An earlier version of this article can be found on BioRxiv.

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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 assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly. As the MinION is approaching a state of maturity, its user community would benefit from a thorough comparative benchmarking effort of de novo assembly pipelines in the near future. An earlier version of this article can be found on bioRxiv.

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Mafune, Korena K., Bruce J. Godfrey, Daniel J. Vogt, and Kristiina A. Vogt. "A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer." BioTechniques 68, no. 2 (February 2020): 72–78. http://dx.doi.org/10.2144/btn-2019-0072.

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The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa. To assess capabilities, three fungal mock communities were sequenced, each of which had varying ratios of 16 taxa. The data were processed through our selected pipeline. The MinION recovered all mock community members, when mixed at equal ratios. When a taxon was represented at a lower ratio, it was not recovered or decreased in relative abundance. Despite high error rates, highly accurate consensus sequences can be derived. This methodological approach identified all mock community taxa, demonstrating the MinION can be used as a practical alternative to profile fungal communities.

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Chang, Jia Jin Marc, Yin Cheong Aden Ip, Chin Soon Lionel Ng, and Danwei Huang. "Takeaways from Mobile DNA Barcoding with BentoLab and MinION." Genes 11, no. 10 (September 24, 2020): 1121. http://dx.doi.org/10.3390/genes11101121.

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Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.

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Ip, Camilla L. C., Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, 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 community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.

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Jain, Miten, Ian T. Fiddes, Karen H. Miga, Hugh E. Olsen, Benedict Paten, and Mark Akeson. "Improved data analysis for the MinION nanopore sequencer." Nature Methods 12, no. 4 (February 16, 2015): 351–56. http://dx.doi.org/10.1038/nmeth.3290.

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Seki, Masahide, Eri Katsumata, Ayako Suzuki, Sarun Sereewattanawoot, Yoshitaka Sakamoto, Junko Mizushima-Sugano, Sumio Sugano, et al. "Evaluation and application of RNA-Seq by MinION." DNA Research 26, no. 1 (November 20, 2018): 55–65. http://dx.doi.org/10.1093/dnares/dsy038.

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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 (April 18, 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 bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%–100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.

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Boža, Vladimír, Peter Perešíni, Broňa Brejová, and Tomáš Vinař. "DeepNano-blitz: a fast base caller for MinION nanopore sequencers." Bioinformatics 36, no. 14 (May 6, 2020): 4191–92. http://dx.doi.org/10.1093/bioinformatics/btaa297.

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Abstract Motivation Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications. Results We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human–pathogen runs). Availability and implementation DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz. Contact vladimir.boza@fmph.uniba.sk Supplementary information Supplementary data are available at Bioinformatics online.

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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 novoerror correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

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Preul, MarkC, Arpan Patel, Evgenii Belykh, EricJ Miller, LaethL George, NikolayL Martirosyan, and VadimA Byvaltsev. "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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Mikheyev, Alexander S., and Mandy M. Y. Tin. "A first look at the Oxford Nanopore MinION sequencer." Molecular Ecology Resources 14, no. 6 (September 24, 2014): 1097–102. http://dx.doi.org/10.1111/1755-0998.12324.

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Probst-Kepper, Michael, and Jan Buer. "FOXP3 and GARP (LRRC32): the master and its minion." Biology Direct 5, no. 1 (2010): 8. http://dx.doi.org/10.1186/1745-6150-5-8.

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Creasey, Ian. "You are not the first minion to disappoint me." Nature 505, no. 7481 (January 2014): 126. http://dx.doi.org/10.1038/505126a.

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Danielson, Chris. "Minion K. C. Morrison.Aaron Henry of Mississippi: Inside Agitator." American Historical Review 121, no. 3 (June 2016): 988–89. http://dx.doi.org/10.1093/ahr/121.3.988.

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Laver, T., J. Harrison, P. A. O’Neill, K. Moore, A. Farbos, K. Paszkiewicz, and D. J. Studholme. "Assessing the performance of the Oxford Nanopore Technologies MinION." Biomolecular Detection and Quantification 3 (March 2015): 1–8. http://dx.doi.org/10.1016/j.bdq.2015.02.001.

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Walter, Mathias C., Katrin Zwirglmaier, Philipp Vette, Scott A. Holowachuk, Kilian Stoecker, Gelimer H. Genzel, and Markus H. Antwerpen. "MinION as part of a biomedical rapidly deployable laboratory." Journal of Biotechnology 250 (May 2017): 16–22. http://dx.doi.org/10.1016/j.jbiotec.2016.12.006.

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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 (February 18, 2021): 794–804. http://dx.doi.org/10.1111/2041-210x.13561.

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Leggett, Richard M., Cristina Alcon-Giner, Darren Heavens, Shabhonam Caim, Thomas C. Brook, Magdalena Kujawska, Samuel Martin, et al. "Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens." Nature Microbiology 5, no. 3 (December 16, 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 episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.

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Schuele, Leonard, Hayley Cassidy, Erley Lizarazo, Katrin Strutzberg-Minder, Sabine Schuetze, Sandra Loebert, Claudia Lambrecht, et al. "Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples." Viruses 12, no. 12 (November 27, 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 viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.

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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 channel devoted to updates to and analysis of nanopore sequence data.

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Jain, Miten, John R. Tyson, Matthew Loose, Camilla L. C. Ip, David A. Eccles, Justin O'Grady, Sunir Malla, et al. "MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry." F1000Research 6 (May 31, 2017): 760. http://dx.doi.org/10.12688/f1000research.11354.1.

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Background: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichia coli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry. Methods: We computed the error-rate estimates for insertions, deletions, and mismatches in MinION reads. Results: Run-time characteristics of the flow cell and run scripts for R9.0 were similar to those observed for R7.3 chemistry, but with an 8-fold increase in bases per second (from 30 bps in R7.3 and SQK-MAP005 library preparation, to 250 bps in R9.0) processed by individual nanopores, and less drop-off in yield over time. The 2-dimensional (“2D”) N50 read length was unchanged from the prior chemistry. Using the proportion of alignable reads as a measure of base-call accuracy, 99.9% of “pass” template reads from 1-dimensional (“1D”) experiments were mappable and ~97% from 2D experiments. The median identity of reads was ~89% for 1D and ~94% for 2D experiments. The total error rate (miscall + insertion + deletion ) decreased for 2D “pass” reads from 9.1% in R7.3 to 7.5% in R9.0 and for template “pass” reads from 26.7% in R7.3 to 14.5% in R9.0. Conclusions: These Phase 2 MinION experiments serve as a baseline by providing estimates for read quality, throughput, and mappability. The datasets further enable the development of bioinformatic tools tailored to the new R9.0 chemistry and the design of novel biological applications for this technology. Abbreviations: K: thousand, Kb: kilobase (one thousand base pairs), M: million, Mb: megabase (one million base pairs), Gb: gigabase (one billion base pairs).

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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 (August 6, 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 Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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Wei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, Ying-Chin Lin, Cheng-Yang Lee, Tzu-Hao Chang, Ben-Chang Shia, and Jung-Chun Lin. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform." International Journal of Molecular Sciences 21, no. 19 (September 26, 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, bar-coded, and sequenced using the Illumina MiSeq and ONT MinION sequencers and corresponding kits. Mapping of the sequenced amplicon using MinION to the entire 16S rRNA gene was analyzed with the cloud-based EPI2ME algorithm. V3–V4 reads generated using MiSeq were aligned by applying the CLC genomics workbench. More than 90% of sequenced reads generated using distinct sequencers were accurately classified at the genus or species level. The misclassification of sequenced reads at the species level between the two approaches was less substantial as expected. Taken together, the comparative results demonstrate that MinION sequencing platform coupled with the corresponding algorithm could function as a practicable strategy in classifying bacterial community to the species level.

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Irinyi, Laszlo, Yiheng Hu, Minh Thuy Vi Hoang, Lana Pasic, Catriona Halliday, Menuk Jayawardena, Indira Basu, 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 (November 23, 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. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.

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Ward, Alan C., and Wonyong Kim. "MinION™: New, Long Read, Portable Nucleic Acid Sequencing Device." Journal of Bacteriology and Virology 45, no. 4 (2015): 285. http://dx.doi.org/10.4167/jbv.2015.45.4.285.

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Lanfear, R., M. Schalamun, D. Kainer, W. Wang, and B. Schwessinger. "MinIONQC: fast and simple quality control for MinION sequencing data." Bioinformatics 35, no. 3 (July 23, 2018): 523–25. http://dx.doi.org/10.1093/bioinformatics/bty654.

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Spatz, Stephen J., Maricarmen Garcia, Sylva Riblet, Teresa A. Ross, Jeremy D. Volkening, Tonya L. Taylor, Taejoong Kim, and Claudio L. Afonso. "MinION sequencing to genotype US strains of infectious laryngotracheitis virus." Avian Pathology 48, no. 3 (March 11, 2019): 255–69. http://dx.doi.org/10.1080/03079457.2019.1579298.

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Cao, Minh Duc, Devika Ganesamoorthy, Matthew A. Cooper, and Lachlan J. M. Coin. "Realtime analysis and visualization of MinION sequencing data with npReader." Bioinformatics 32, no. 5 (November 10, 2015): 764–66. http://dx.doi.org/10.1093/bioinformatics/btv658.

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Liau, Yusmiati, Simone L. Cree, Simran Maggo, Allison L. Miller, John F. Pearson, Patrick A. Gladding, and Martin A. Kennedy. "A multiplex pharmacogenetics assay using the MinION nanopore sequencing device." Pharmacogenetics and Genomics 29, no. 9 (November 2019): 207–15. http://dx.doi.org/10.1097/fpc.0000000000000385.

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Matern, Benedict, Mathijs Groeneweg, Thuur Slangen, Marcel G. Tilanus, and Christien Voorter. "P095 ABO blood group typing with the Oxford nanopore minion." Human Immunology 78 (September 2017): 122. http://dx.doi.org/10.1016/j.humimm.2017.06.155.

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Setiadi, Ozi. "LEGITIMASI KEPEMIMPINAN BANI QURAISY." Riwayah : Jurnal Studi Hadis 5, no. 1 (June 24, 2019): 143. http://dx.doi.org/10.21043/riwayah.v5i1.5588.

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Kepemimpinan Bani Quraisy mendapatkan perhatian khusus dari Rasulullah Muhammad Saw. Perhatian ini dituangkan dalam hadis yang banyak diriwayatkan oleh perawi hadis. Imam Ahmad, Imam Bukhari, dan Imam Muslim adalah ulama-ulama yang juga meriwayatkan hadis tersebut. Hal ini juga mendapatkan perhatian dari pemikir Islam. Al-Farabi, Ibnu Thaimiyyah, Al Farabi dan Nashiruddin Thusi memiliki pendapat yang berbeda. Secara umum dapat disimpulkan pendapat para ulama hadis dan pemikir Islam bahwa; Pertama, secara tekstual tidak terjadi perdebatan tentang hadis kepemimpinan Bani Quraisy dan pemikir Islam menerima hal ini. Kedua, Bani Quraisy menjadi ketentuan yang sunatullah, menjadi pemimpin dalam cakupan global, tetapi tidak regional. Ketiga, kepemimpinan dalam cakupan regional memberikan peluang bagi pemimpin yang berasal dari non Bani Quraisy untuk menduduki jabatan kepempimpinan. Keempat, kesempatan untuk menjadi pemimpin bagi kalangan non Bani Quraisy harus tetap memperhatikan kriteria-kriteria atau syarat-syarat menjadi pemimpin. Mulai dari siapa yang memilih kemudian siapa yang akan dipilih..

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Zaini, Ahmad. "NILAI-NILAI DAKWAH DALAM NOVEL “BUMI CINTA” KARYA HABIBURRAHMAN EL-SHIRAZY." AT-TABSYIR: Jurnal Komunikasi Penyiaran Islam 6, no. 1 (June 30, 2019): 74. http://dx.doi.org/10.21043/at-tabsyir.v6i1.5596.

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Dakwah bertujuan untuk menumbuhkan pengertian, kesadaran, penghayatan, dan pengaplikasian terhadap ajaran agama yang dibawa oleh para dai. Novel sebagai media cetak dapat dijadikan sebagai sarana dakwah untuk menyebarkan pesan-pesan kedamaian dan kesejukan bagi para pembacanya. Tulisan ini bertujuan untukmengetahui kandungan makna nilai dakwah novel Bumi Cinta karya Habiburrahman El-Shirazy dan mengeksplorasi muatan dakwah yang terkandung dalam Bumi Cinta karya Habiburrahman El Shirazy. Hasil penelitian dalam novel ini tentang nilai-nilai dakwah terlihat dalam tokoh Ayyas yang digambarkan sebagai sosok yang disiplin dalam menjalankan ibadah, jujur, pekerja keras, suka menolong orang lain, bersyukur dan sabar dalam menjalani kehidupan di negara yang liberal. Hidup di negara liberal tidak lantas membuat kita terhanyut dengan kehidupan di dalamnya, namun harus tetap menjaga ajaran agama dan adat ketimuran yang dimilikinya. Novel yang bercerita tentang kehidupan mahasiwa yang bernama Ayyas yang sedang kuliah di Rusia dapat dijadikan sebagai dasar dan gambaran bahwa tinggal di negara-negara yang memiliki prinsip kebebasan merupakan tantangan yang berat sehingga harus disikapi dengan bijak.

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Deshpande, Reed, Sullivan, Kerkhof, Beigel, and Wade. "Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)." Genes 10, no. 8 (July 30, 2019): 578. http://dx.doi.org/10.3390/genes10080578.

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Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.

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Journal articles on the topic 'Minion'

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