title: Assessing the performance of the Oxford Nanopore Technologies MinION.
abstract: The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
authors.forename: T
authors.initials: T
authors.lastname: Laver
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
authors.forename: J
authors.initials: J
authors.lastname: Harrison
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: P A
authors.initials: PA
authors.lastname: O'Neill
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: K
authors.initials: K
authors.lastname: Moore
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: A
authors.initials: A
authors.lastname: Farbos
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: K
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
authors.forename: D J
authors.initials: DJ
authors.lastname: Studholme
keywords: DNA sequencing; MinION; NRPS, non-ribosomal peptide synthase; Nanopore; ONT, Oxford Nanopore Technologies