A complete bacterial genome assembled de novo using only nanopore sequencing data (original) (raw)

Nature Methods volume 12, pages 733–735 (2015)Cite this article

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Abstract

We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then corrected by a multiple-alignment process; (ii) corrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a probabilistic model of the signal-level data. The assembly reconstructs gene order and has 99.5% nucleotide identity.

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Acknowledgements

Data analysis was performed on the Medical Research Council Cloud Infrastructure for Microbial Bioinformatics (CLIMB) cyberinfrastructure. N.J.L. is funded by a Medical Research Council Special Training Fellowship in Biomedical Informatics. J.Q. is funded by the UK National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre. J.T.S. is supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario. We thank the staff of Oxford Nanopore for technical help and advice during the MinION Access Programme. We are grateful to the EU COST action ES1103, whose funding allowed us to attend a hackathon that kick-started the work presented here. We thank L. Parts for comments on the manuscript and H. Eno for help with proofreading.

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Authors and Affiliations

  1. Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
    Nicholas J Loman & Joshua Quick
  2. Ontario Institute for Cancer Research, Toronto, Ontario, Canada
    Jared T Simpson
  3. Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
    Jared T Simpson

Authors

  1. Nicholas J Loman
  2. Joshua Quick
  3. Jared T Simpson

Contributions

N.J.L. and J.T.S. conceived the project. N.J.L., J.Q. and J.T.S. implemented the Nanocorrect pipeline. J.T.S. conceived and implemented the Nanopolish pipeline. J.Q. generated the nanopore E. coli sequence data. N.J.L. and J.T.S. performed de novo assembly and analyzed the results. N.J.L. and J.T.S. wrote the manuscript. All authors approved the final manuscript.

Corresponding author

Correspondence toJared T Simpson.

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Competing interests

N.J.L. and J.T.S. are members of the MinION Access Programme (MAP). N.J.L. has received free-of-charge reagents for nanopore sequencing presented in this study. N.J.L., J.Q. and J.T.S. have received travel and accommodation expenses to speak at an Oxford Nanopore–organized symposium. N.J.L. and J.Q. have ongoing research collaborations with Oxford Nanopore but do not receive financial compensation for this.

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Loman, N., Quick, J. & Simpson, J. A complete bacterial genome assembled de novo using only nanopore sequencing data.Nat Methods 12, 733–735 (2015). https://doi.org/10.1038/nmeth.3444

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