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Nanopore sequencing technology, bioinformatics and applications

Nature Biotechnology volume 39, pages 1348–1365 (2021)Cite this article

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Abstract

Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.

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Fig. 1: Principle of nanopore sequencing.
Fig. 2: ONT sequencing data improvement over time.
Fig. 3: Library preparation workflow for ONT sequencing.
Fig. 4: Analyses of ONT sequencing data.
Fig. 5: Applications of ONT sequencing.

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Acknowledgements

K.F.A., Yunhao Wang, Y.Z., A.B. and Yuru Wang are grateful for support from an institutional fund of the Department of Biomedical Informatics, The Ohio State University, and the National Institutes of Health (R01HG008759, R01HG011469 and R01GM136886). The authors apologize to colleagues whose studies were not cited due to length and reference constraints. The authors also apologize that the very latest research published during the publication process of this article was not included. We would like to thank K. Aschheim and G. Riddihough for critical reading and editing of the manuscript.

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  1. These authors contributed equally: Yunhao Wang, Yue Zhao, Audrey Bollas.

Authors and Affiliations

  1. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA

    Yunhao Wang, Yue Zhao, Audrey Bollas, Yuru Wang & Kin Fai Au

  2. Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA

    Yue Zhao & Kin Fai Au

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Contributions

K.F.A. designed the outline of the article. Yunhao Wang and A.B. collected information and prepared the materials for the ‘Technology development’ and ‘Data analysis’ sections. Y.Z. collected information and prepared the materials for the ‘Applications of nanopore sequencing’ section. K.F.A., Yunhao Wang, Y.Z. and A.B. wrote and revised the main text. Yuru Wang collected the references for the ‘Applications of nanopore sequencing’ section and prepared Fig. 1.

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Correspondence to Kin Fai Au.

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K.F.A. was invited by ONT to present at the conference London Calling 2020.

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Wang, Y., Zhao, Y., Bollas, A. et al. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 39, 1348–1365 (2021). https://doi.org/10.1038/s41587-021-01108-x

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