MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry
Open accessAbstract
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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The error rate of second-generation synthesis and sequencing technology is less than 5%, while that of third-generation is about 10-15%.
“The error rate of the second-generation synthesis and sequencing technology is less than 5%, while that of the third-generation is about 10–15% [31, 32].”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [32]
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- Authors
- Jain, M., Tyson, J. R., Loose, M., Ip, C. L. C., Eccles, D. A., O'Grady, J., Malla, S., Leggett, R. M., Wallerman, O., Jansen, H. J., Zalunin, V., Birney, E., Brown, B. L., Snutch, T. P., Olsen, H. E., & MinION Analysis and Reference Consortium
- Affiliations
- University of California, Santa Cruz (US)
- University of British Columbia (CA)
- University of Nottingham (GB)
- Centre for Human Genetics (GB)
- Malaghan Institute of Medical Research (NZ)
- Norwich Research Park (GB)
- Uppsala University (SE)
- ZF Screens (Netherlands) (NL)
- European Bioinformatics Institute (GB)
- Virginia Commonwealth University (US)
- Corresponding author
- Loose, Matthew
- Ip, Camilla L.C.
- Brown, Bonnie L.
- Snutch, Terrance P.
- ORCID
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2017-05-31
- Volume
- 6
- Pages
- 760
- ISSN
- 2046-1402 (ISSN-L)
- PMC
- PMC5538040
- OpenAlex
- W2620002992
- Cited by
- 140
- References
- 11
- Citations by year
- 2026: 4 · 2025: 13 · 2024: 13 · 2023: 12 · 2022: 10 · 2021: 21 · 2020: 20 · 2019: 18 · 2018: 24 · 2017: 5
- FWCI
- 7.45
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- F1000Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Human Genome Research Institute (HG007827, HG006321)
- Biotechnology and Biological Sciences Research Council (BB/J010375/1, BB/M020061/1)
- Canadian Institutes of Health Research (10677)
- Genome British Columbia
- Michael Smith Foundation for Health Research
- Brain Canada
- Rosetrees Trust (A749)
- National Science Foundation (DEB-1355059)
- Wellcome Trust (090532/Z/09/Z)
- Koerner Foundation
- Antimicrobial Resistance Cross Council Initiative (MR/N013956/1)
- E o R Börjessons Foundation
- 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 › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- Oxford Nanopore MinION, nanopore sequencing, long-read sequencing, Escherichia coli K-12, whole genome sequencing, sequencing error rate, base calling accuracy, sequencing throughput, reference data
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