title: A complete bacterial genome assembled de novo using only nanopore sequencing data.
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.
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Joshua
authors.initials: J
authors.lastname: Quick
authors.affiliation: 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping / Q000379:methods; D048168:Escherichia coli K12 / Q000235:genetics*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software