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Nat Methods. 2015 Aug;12(8):733-5. doi: 10.1038/nmeth.3444. Epub 2015 Jun 15.

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

Author information

1
Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
2
1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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.

PMID:
26076426
DOI:
10.1038/nmeth.3444
[Indexed for MEDLINE]

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