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Oxford Nanopore MinION Sequencing and Genome Assembly
2016
Genomics, Proteomics & Bioinformatics
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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
2018
Scientific Data
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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]
2019
bioRxiv
pre-print
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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
2019
BMC Bioinformatics
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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]
2016
bioRxiv
pre-print
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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
2017
GigaScience
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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
2019
American Journal of Tropical Medicine and Hygiene
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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
2015
GigaScience
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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
2016
Scientific Reports
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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]
2015
bioRxiv
pre-print
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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
2021
BMC Research Notes
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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
2020
Microbiology Resource Announcements
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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
2018
Surgical neurology international
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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
2018
Microbiology Resource Announcements
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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
2021
Microbiology Resource Announcements
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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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