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Oxford Nanopore MinION Sequencing and Genome Assembly

Hengyun Lu, Francesca Giordano, Zemin Ning
2016 Genomics, Proteomics & Bioinformatics  
In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT).  ...  The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.  ...  Acknowledgments We would like to thank the MinION Analysis and Reference Consortium (MARC) for sharing the ONT data.  ... 
doi:10.1016/j.gpb.2016.05.004 pmid:27646134 pmcid:PMC5093776 fatcat:6fim4654yncq3pb67nnqquaj6m

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux, Corinne Da Silva, Léo d'Agata, Arnaud Couloux, Elise J Gay, Benjamin Istace, Nicolas Lapalu, Arnaud Lemainque, Juliette Linglin, Benjamin Noel, Patrick Wincker, Corinne Cruaud (+3 others)
2018 Scientific Data  
Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads.  ...  Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3.  ...  Acknowledgements The authors are grateful to Oxford Nanopore Technologies Ltd for providing early access to the MinION device through the MinION Access Programme, and we thank the staff of Oxford Nanopore  ... 
doi:10.1038/sdata.2018.235 pmid:30398473 pmcid:PMC6219404 fatcat:noln5n2n3ndpdbbn5sixkjzlj4

NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly [article]

Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores
2019 bioRxiv   pre-print
AbstractBackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe present NanoDJ  ...  , a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices.  ...  data was generated in house as part of an independent study using the Rapid Sequencing kit (SQK-RAD001) (Oxford Nanopore Technologies Ltd., Oxford, UK) in a single MinION 22-h run.  ... 
doi:10.1101/586842 fatcat:2vyy2smntvavnpj3lvuud2fngy

NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly

Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores
2019 BMC Bioinformatics  
The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.  ...  Results: We present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices.  ...  Genome assembly and comparison Depending on the application, sequence data can be aligned against reference sequences or used for genome assembly using diverse methods.  ... 
doi:10.1186/s12859-019-2860-z fatcat:4pliw7jdanfjrlqsn65vpfpqo4

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer [article]

Benjamin Istace, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen (+3 others)
2016 bioRxiv   pre-print
Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small and low-cost single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments.  ...  The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a matter of seconds.  ...  BI, SD, 520CCR, AL, SE, PW and JMA are part of the MinION Access Programme (MAP). 521 Abbreviations 523 ONT: Oxford Nanopore Technology; SMRT: Single-Molecule Real-Time Sequencing; USB: 524 Universal Serial  ... 
doi:10.1101/066613 fatcat:lq5oey5kc5akhithash64be2iy

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Benjamin Istace, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen (+3 others)
2017 GigaScience  
BI, SD, 520CCR, AL, SE, PW and JMA are part of the MinION Access Programme (MAP). 521 Abbreviations 523 ONT: Oxford Nanopore Technology; SMRT: Single-Molecule Real-Time Sequencing; USB: 524 Universal Serial  ...  GL, PW, JS and JMA supervised the study. 531 532 device through the MinION Access Programme (MAP) and we thank the staff of Oxford 537 Nanopore Technology Ltd for technical help.  ... 
doi:10.1093/gigascience/giw018 pmid:28369459 pmcid:PMC5466710 fatcat:erld33xdsvgxrk5ev36234oyuy

Oxford Nanopore MinION Sequencing Enables Rapid Whole Genome Assembly of Rickettsia typhi in a Resource-Limited Setting

Ivo Elliott, Elizabeth M. Batty, Damien Ming, Matthew T. Robinson, Pruksa Nawtaisong, Mariateresa de Cesare, Paul N. Newton, Rory Bowden
2019 American Journal of Tropical Medicine and Hygiene  
The infrastructure challenges and costs of next-generation sequencing have been largely overcome, for many sequencing applications, by Oxford Nanopore Technologies' portable MinION sequencer.  ...  Filtering based on the known error profile of MinION data improved the accuracy of the nanopore-only assembly.  ...  Oxford Nanopore Technologies' (ONT) MinION sequencer is a portable device for DNA and RNA sequencing that generates data for local analysis, in real time.  ... 
doi:10.4269/ajtmh.19-0383 pmid:31820709 pmcid:PMC7008338 fatcat:6tjblk7thjhu5borokeaghap7i

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Judith Risse, Marian Thomson, Sheila Patrick, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter, Mick Watson
2015 GigaScience  
Results: We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms.  ...  The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.  ...  Acknowledgements The authors would like to thank Oxford Nanopore for granting Edinburgh Genomics access to the MinION Access Programme (MAP).  ... 
doi:10.1186/s13742-015-0101-6 pmid:26640692 pmcid:PMC4670535 fatcat:oeqewc57vvautpv5pdpowf2cii

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

Stéphane Deschamps, Joann Mudge, Connor Cameron, Thiruvarangan Ramaraj, Ajith Anand, Kevin Fengler, Kevin Hayes, Victor Llaca, Todd J. Jones, Gregory May
2016 Scientific Reports  
The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded  ...  While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial  ...  We also wish to thank Oxford Nanopore Technologies for granting us access to the MinION Early Access Program (MAP), in particular Spike Willcocks for his early support and guidance, as well as all members  ... 
doi:10.1038/srep28625 pmid:27350167 pmcid:PMC4923883 fatcat:6bw2t73o4bazvndr7oqfvviqye

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data [article]

Judith Risse, Marian Thomson, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter, Mick Watson
2015 bioRxiv   pre-print
Results We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms.  ...  The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.  ...  Acknowledgements The authors would like to thank Oxford Nanopore for granting Edinburgh Genomics access to the MinION Access Programme (MAP).  ... 
doi:10.1101/024323 fatcat:i4lakiubmfgcjoxj3j2vc4hl6i

The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing

Paula Moolhuijzen, Pao Theen See, Caroline S. Moffat
2021 BMC Research Notes  
However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived  ...  Results The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%.  ...  Acknowledgements We thank the Australian grain growers for their continued support of research through the Grains Research and Development Corporation (GRDC) and the Australian Government National Collaborative  ... 
doi:10.1186/s13104-021-05751-0 pmid:34454585 fatcat:rzyqab4cxzeqtkdjjarzzmwdhu

Complete Genome Sequence of Phytobacter diazotrophicus Strain UAEU22, a Plant Growth-Promoting Bacterium Isolated from the Date Palm Rhizosphere

Yasmeen Salha, Naganeeswaran Sudalaimuthuasari, Biduth Kundu, Raja S. AlMaskari, AlReem S. Alkaabi, Khaled M. Hazzouri, Synan F. AbuQamar, Khaled A. El-Tarabily, Khaled M. A. Amiri, David A. Baltrus
2020 Microbiology Resource Announcements  
Here, we present a complete circular genome (5.4 Mb) and a plasmid (104,972 bp) of the plant growth-promoting bacterium Phytobacter diazotrophicus strain UAEU22, isolated from date palm rhizosphere in  ...  Annotation of the genome resulted in 5,229 predicted genes.  ...  ACKNOWLEDGMENT This work was supported by the Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University.  ... 
doi:10.1128/mra.00499-20 pmid:32554791 fatcat:fypc344chjbw3ew2vrw6shy7ga

MinION rapid sequencing: Review of potential applications in neurosurgery

MarkC Preul, Arpan Patel, Evgenii Belykh, EricJ Miller, LaethL George, NikolayL Martirosyan, VadimA Byvaltsev
2018 Surgical neurology international  
Results: The Oxford MinION nanopore sequencing technology has had successful applications within clinical microbiology, human genome sequencing, and cancer genotyping across multiple specialties.  ...  Methods: A literature search was conducted for publications containing the keywords of Oxford MinION, nanopore sequencing, brain tumor, glioma, whole genome sequencing (WGS), epigenomics, molecular neuropathology  ...  Key Words: DNA, MinION, nanopore, neurosurgery, sequencing, tumor Oxford MinION device Sequencing Understanding nanopore technology and the molecular science behind the Oxford MinION may present a daunting  ... 
doi:10.4103/sni.sni_55_18 pmid:30159201 pmcid:PMC6094492 fatcat:54goaewnivgvzitr3fl26c5yvq

Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing

Valérie Bouchez, Sarah Louise Baines, Sophie Guillot, Sylvain Brisse, Vincent Bruno
2018 Microbiology Resource Announcements  
Sequences were obtained using a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq 500 sequence data.  ...  Here, we describe the complete genome sequences of two Bordetella pertussis strains, FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for  ...  Illumina raw reads files were previously published (1) under BioSample accession numbers ERS1869884 and ERS1869859, and Oxford Nanopore Technologies MinION raw reads files were deposited in SRA under the  ... 
doi:10.1128/mra.01207-18 pmid:30533789 pmcid:PMC6256476 fatcat:vkvqmk2uszenrncc4izduycfku

Complete Genome Sequences of Pseudomonas atacamensis Strain SM1 and Pseudomonas toyotomiensis Strain SM2, Isolated from the Date Palm Rhizosphere

Yassine Elmahi, Mohammed Saeed Alshamsi, Naganeeswaran Sudalaimuthuasari, Biduth Kundu, Raja S AlMaskari, Khaled M Hazzouri, Subha Chandran, Shahana Sehar Malik, Sunil Mundra, Khaled M A Amiri
2021 Microbiology Resource Announcements  
Here, we announce the complete genome sequences of two phosphate-solubilizing rhizobacteria, Pseudomonas atacamensis strain SM1 (genome size, ∼5.9 Mb) and Pseudomonas toyotomiensis strain SM2 (genome size  ...  ACKNOWLEDGMENT This work was supported by the Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University.  ...  Oxford Nanopore WGS libraries were prepared using a ligation sequencing kit (SQK-LSK 109) and sequenced using the Oxford Nanopore MinION system (flow cell, FLO-MIN106D R9.4 revision D chip).  ... 
doi:10.1128/mra.00253-21 pmid:33958397 fatcat:ppaprji2ybe4fdjg5o46ey4cuy
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