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.
Bibliographical noteFunding 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.
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