title: NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
abstract: BACKGROUND
  The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis--something that is extremely important given the speed with which the platform is evolving.
  
  
  RESULTS
  NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.
  
  
  METHODS
  NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub--see program documentation https://documentation.tgac.ac.uk/display/NANOOK.
  
  
  BACKGROUND
  richard.leggett@tgac.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Leggett
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.
authors.forename: Darren
authors.initials: D
authors.lastname: Heavens
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Clark
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Davey
mesh_terms: D001483:Base Sequence; D000068598:Data Accuracy; D048168:Escherichia coli K12 / Q000235:genetics; D058608:Nanopores; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software