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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

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Jain, Miten, Olsen, Hugh E., Paten, Benedict, Akeson, Mark·2016·Genome Biology
DOI 10.1186/s13059-016-1103-0PMC PMC5124260
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Abstract

Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.

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Crossref · 10.1186/s13059-016-1103-0

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  • New genome assemblies have been arriving at a rapidly increasing pace, due to decreases in sequencing costs and improvements in third-generation sequencing technologies.

    “New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1–3.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [3]

    The De novo assembly section (page unavailable) describes how nanopore sequencing has enabled new assembly methods and reports a genome assembled using only MinION data. The Conclusions (page unavailable) say MinION performance improved rapidly. Neither passage establishes that new genome assemblies are arriving at a rapidly increasing pace or attributes that pace to falling sequencing costs. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to long-read sequencing technologies, DNA proximity ligation sequencing techniques, and genome sequencing consortia.

    “Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [52]

    The Outlook’s “Read length” section identifies PacBio and MinION as long-read technologies, and “De novo assembly” describes a bacterial genome assembled using MinION data. The paper also cites MinION’s cost as an advantage, but these passages do not establish the broader claim that long-read technologies have made genome sequencing and assembly increasingly affordable and computationally tractable. Hi-C and consortium efforts are attached to other citations in the citing sentence and are not assessed here. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 65

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Cited by

Sorted by citations

Authors
Jain, M., Olsen, H. E., Paten, B., & Akeson, M.
Affiliations
University of California, Santa Cruz (US)
Corresponding author
Akeson, Mark
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2016-11-25
Volume
17
Issue
1
Pages
239-239
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-016-1103-0
PMC
PMC5124260
OpenAlex
W2550586733
Cited by
1,588
References
1
Citations by year
2026: 147 · 2025: 177 · 2024: 191 · 2023: 167 · 2022: 151 · 2021: 240 · 2020: 168 · 2019: 148 · 2018: 131 · 2017: 64 · 2016: 2 · 2014: 1
FWCI
49.12
Type
journal article
Language
en
Update notices
correction (2016-12-13)
Open access
Licence
cc-by
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
National Human Genome Research Institute (US) (HG007827, U54HG007990, HG006321)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords
Oxford Nanopore MinION, nanopore DNA sequencing, portable sequencing, long-read sequencing, genomics applications
MeSH terms
Algorithms, Aneuploidy, DNA, Humans, Reproducibility of Results, Computational Biology, Genomics, Nanopores, High-Throughput Nucleotide Sequencing

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