title: Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.
abstract: Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistantEnterobacter kobeiisolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion in the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50 %, 80 % and 90 % of MinION pass reads were generated in the first 6, 9 and 12 h, respectively. Using data from the first 6 h alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 h generated similar assemblies to that from 48 h sequencing. Assemblies were generated in 2 h using Canu, indicating that going from isolate to assembled data is possible in less than 48 h. MinION data identified that genes responsible for resistance were carried by two plasmids encoding resistance to carbapenem and to sulphonamides, rifampicin and aminoglycosides, respectively.
authors.affiliation: 1​Department of Medicine, University of Cambridge, Level 5, Addenbrookes Hospital, CB2 0QQ Cambridge, UK.
authors.forename: Kim
authors.initials: K
authors.lastname: Judge
authors.affiliation: 2​Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.affiliation: 1​Department of Medicine, University of Cambridge, Level 5, Addenbrookes Hospital, CB2 0QQ Cambridge, UK.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: 2​Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: Tracey
authors.affiliation: 2​Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.affiliation: 2​Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: 3​London School of Hygiene and Tropical Medicine, University of London, Keppel St, WC1E 7HT London, UK.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004754:Enterobacter / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008829:Microbiology / Q000592:standards / Q000639:trends*; D010957:Plasmids / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software / Q000592:standards*
keywords: MinION; antimicrobial resistance; assembly; long reads; plasmid; software