A complete bacterial genome assembled de novo using only nanopore sequencing data

Nicholas J. Loman, Joshua Quick, Jared T. Simpson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

545 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)733-735
Number of pages3
JournalNature Methods
Volume12
Issue number8
DOIs
Publication statusPublished - 30 Jul 2015
Externally publishedYes

Bibliographical note

Funding Information:
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.

Publisher Copyright:
© 2015 Nature America, Inc. All rights reserved.

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