title: Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.
abstract: The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) "2D" sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy.
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Deschamps
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Connor
authors.initials: C
authors.lastname: Cameron
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Thiruvarangan
authors.initials: T
authors.lastname: Ramaraj
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Ajith
authors.initials: A
authors.lastname: Anand
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Fengler
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Hayes
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Llaca
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Jones
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: May
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics*; D030541:Databases, Genetic