Brief Communication | Published:

Real-time selective sequencing using nanopore technology

Nature Methods volume 13, pages 751754 (2016) | Download Citation

Abstract

The Oxford Nanopore Technologies MinION sequencer enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores. To directly select molecules for sequencing, we used dynamic time warping to match reads to reference sequences. We demonstrate our open-source Read Until software in real-time selective sequencing of regions within small genomes, individual amplicon enrichment and normalization of an amplicon set.

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Primary accessions

European Nucleotide Archive

Referenced accessions

European Nucleotide Archive

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Acknowledgements

This work was supported by BBSRC TRDF award BB/M020061/1. The authors thank T. Evans for comments and discussion on the manuscript and figures, N. Loman and J. Quick for helpful discussions, advice and motivation and M. Blythe for discussions. We also thank ONT for access to the Read Until API and helpful discussions and support.

Author information

Affiliations

  1. School of Life Sciences, University of Nottingham, Nottingham, UK.

    • Matthew Loose
    • , Sunir Malla
    •  & Michael Stout

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Contributions

M.L. conceived and designed the project, wrote the code, ran sequencing, performed analysis and wrote the manuscript. M.S. carried out analysis and wrote and contributed to code and contributed to the manuscript. S.M. generated libraries, ran sequencing and contributed to the manuscript.

Competing interests

M.L. is a member of the MinION access program (MAP) and has received free-of-charge flowcells and kits for nanopore sequencing and travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences.

Corresponding author

Correspondence to Matthew Loose.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Tables 1–4

Zip files

  1. 1.

    Supplementary Software

    Read Until code and accessory files

About this article

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DOI

https://doi.org/10.1038/nmeth.3930

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