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781“…However, existing methods that employ a subsequence dynamic time warping (sDTW) algorithm for this problem are too computationally intensive that a massive workstation with dozens of CPU cores still struggles to keep up with the data rate of a mobile phone–sized MinION sequencer. RESULTS: In this article, we present Hardware Accelerated Read Until (HARU), a resource-efficient hardware–software codesign-based method that exploits a low-cost and portable heterogeneous multiprocessor system-on-chip platform with on-chip field-programmable gate arrays (FPGA) to accelerate the sDTW-based Read Until algorithm. …”
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782por Bird, Jennifer E., Nguyen, Claire VT, Hohl, Sarah D., D’Angelo, Heather, Pauk, Danielle, Adsit, Robert T., Fiore, Michael, Minion, Mara, McCarthy, Danielle, Rolland, BetsyEnlace del recurso
Publicado 2023
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783“…The CRKP isolate KP424 co-carrying bla(NDM-1) and bla(KPC-2), recovered from a stool specimen, was identified by the NG-Test Carba 5 test, and the genome sequence was further determined by using Nanopore MinION and Illumina NovaSeq 6000 technologies. The genome sequences of the CRKP strains carrying multiple carbapenemase genes were further retrieved from the NCBI GenBank database. …”
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784por Fortini, Daniela, García-Fernández, Aurora, Lucarelli, Claudia, Dionisi, Anna Maria, Arena, Sergio, Owczarek, Slawomir, Equestre, Michele, Carattoli, Alessandra, Sacco, Federica, Rossi, Stefano, Ortenzi, Roberta, Primavilla, Sara, Villa, Laura“…Whole-genome sequencing (WGS) was performed using both the NovaSeq 6000 S4 PE150 XP platform (Illumina, San Diego, CA, USA) and MinION (Oxford Nanopore). The S. Rissen 4_29_19 strain harboured two plasmids: a pKpQIL-like plasmid carrying the bla(KPC-3) resistance gene in a Tn4401a transposon (pKPC_4_29_19), and a ColE-like plasmid (p4_4_29_19) without resistance genes, highly prevalent among Enterobacterales. …”
Publicado 2023
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785por Wan, Yu, Sabnis, Akshay, Mumin, Zaynab, Potterill, Isabelle, Jauneikaite, Elita, Brown, Colin S., Ellington, Matthew J., Edwards, Andrew, Sriskandan, Shiranee“…Genomes of derived isolates were sequenced on Illumina and Nanopore MinION systems. Genetic variation between isolates was determined based on genome assemblies and read mapping. …”
Publicado 2023
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786por Dixon-Woods, Mary, Baker, Richard, Charles, Kathryn, Dawson, Jeremy, Jerzembek, Gabi, Martin, Graham, McCarthy, Imelda, McKee, Lorna, Minion, Joel, Ozieranski, Piotr, Willars, Janet, Wilkie, Patricia, West, MichaelEnlace del recurso
Publicado 2014
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787
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788“…In parallel, we used the Oxford Nanopore Technologies’s (ONT) MinION to resolve full-length defective and wild-type viral genomes. …”
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789por van der Merwe, Marcel, D. Jukes, Michael, Rabalski, Lukasz, Knox, Caroline, K. Opoku-Debrah, John, D. Moore, Sean, Krejmer-Rabalska, Martyna, Szewczyk, Boguslaw, P. Hill, Martin“…Furthermore, the study describes the first complete baculovirus genome to be sequenced with the MinION (Oxford Nanopore, Oxford, UK) platform and the first complete genome sequence of the South African CrleGV isolate.…”
Publicado 2017
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790por Brickwedde, Anja, Brouwers, Nick, van den Broek, Marcel, Gallego Murillo, Joan S., Fraiture, Julie L., Pronk, Jack T., Daran, Jean-Marc G.“…To obtain complete sequences of the MAL loci of this strain, a near-complete genome assembly was generated using the Oxford Nanopore Technology MinION sequencing platform. Except for CHRXII, all sixteen chromosomes were assembled as single contigs. …”
Publicado 2018
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791por Solares, Edwin A., Chakraborty, Mahul, Miller, Danny E., Kalsow, Shannon, Hall, Kate, Perera, Anoja G., Emerson, J. J., Hawley, R. Scott“…Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. …”
Publicado 2018
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792por Warwick-Dugdale, Joanna, Solonenko, Natalie, Moore, Karen, Chittick, Lauren, Gregory, Ann C., Allen, Michael J., Sullivan, Matthew B., Temperton, Ben“…The ‘VirION’ (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. …”
Publicado 2019
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793por Hadjadj, Linda, Baron, Sophie Alexandra, Olaitan, Abiola Olumuyiwa, Morand, Serge, Rolain, Jean-Marc“…Moreover, whole genome sequencing (WGS) combining Illumina (MiSeq) and Oxford Nanopore technologies (MinION) was realized to obtain closed genomes and plasmids. …”
Publicado 2019
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794por Tsybina, Polly, Hennink, Maurice, Diener, Tania, Minion, Jessica, Lang, Amanda, Lavoie, Stephanie, Kim, John, Wong, AlexanderEnlace del recurso
Publicado 2020
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795por Feodorova, Valentina A., Zaitsev, Sergey S., Khizhnyakova, Mariya A., Saltykov, Yury V., Evstifeev, Vitaliy V., Khusainov, Fidail M., Yakovlev, Sergey I., Larionova, Olga S., Motin, Vladimir L.“…The results were obtained by using standard protocols of sequencing with the Illumina HiSeq 2500 and Oxford Nanopore MinION technology that generated 3.88 GB and 3.08 GB of raw data, respectively. …”
Publicado 2020
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796por Roberts, Leah W., Catchpoole, Elizabeth, Jennison, Amy V., Bergh, Haakon, Hume, Anna, Heney, Claire, George, Narelle, Paterson, David L., Schembri, Mark A., Beatson, Scott A., Harris, Patrick N. A.“…Six isolates were additionally sequenced using Oxford Nanopore MinION to generate long-reads and fully characterize the context of the bla (IMP-4) gene. …”
Publicado 2019
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797por Finton, Misti D., Meisal, Roger, Porcellato, Davide, Brandal, Lin T., Lindstedt, Bjørn-Arne“…Phenotypic resistance to 18 antimicrobial agents was assessed and isolates were subjected to whole genome sequencing through a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results revealed the presence of β-lactamase and ESBL-producing Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and a Paraburkholderia spp. …”
Publicado 2020
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798“…A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. …”
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799por den Drijver, Evert P. M., Stohr, Joep J. J. M., Verweij, Jaco J., Verhulst, Carlo, Velkers, Francisca C., Stegeman, Arjan, Kluytmans-van den Bergh, Marjolein F. Q., Kluytmans, Jan A. J. W.“…Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. …”
Publicado 2020
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800“…Analyses of escape mutants revealed that insertion sequences (ISs) carrying promoters were inserted between the Pu promoter and the bamA gene on the complemented plasmid. MinION deep sequencing of the plasmids extracted from the escape mutants enabled the identification of three types of ISs involved in the emergence of escape mutants, suggesting a strategy for reducing it. …”
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