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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Contig Mapping / methods
  • Escherichia coli K12 / genetics*
  • Genome, Bacterial*
  • High-Throughput Nucleotide Sequencing / methods
  • Nanopores*
  • Nanotechnology / methods*
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Software