title: Realtime analysis and visualization of MinION sequencing data with npReader.
abstract: The recently released Oxford Nanopore MinION sequencing platform presents many innovative features opening up potential for a range of applications not previously possible. Among these features, the ability to sequence in real-time provides a unique opportunity for many time-critical applications. While many software packages have been developed to analyze its data, there is still a lack of toolkits that support the streaming and real-time analysis of MinION sequencing data.
  
  
  
  We developed npReader, an open-source software package to facilitate real-time analysis of MinION sequencing data. npReader can simultaneously extract sequence reads and stream them to downstream analysis pipelines while the samples are being sequenced on the MinION device. It provides a command line interface for easy integration into a bioinformatics work flow, as well as a graphical user interface which concurrently displays the statistics of the run. It also provides an application programming interface for development of streaming algorithms in order to fully utilize the extent of nanopore sequencing potential.
  
  
  
  npReader is written in Java and is freely available at https://github.com/mdcao/npReader
  
  
  
  m.cao1@uq.edu.au or l.coin@imb.uq.edu.au.
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia and.
authors.forename: Minh Duc
authors.initials: MD
authors.lastname: Cao
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia and.
authors.forename: Devika
authors.initials: D
authors.lastname: Ganesamoorthy
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia and.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cooper
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia and Department of Genomics of Common Disease, Imperial College London, London W12 0NN, UK.
authors.forename: Lachlan J M
authors.initials: LJ
authors.lastname: Coin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D058608:Nanopores; D017422:Sequence Analysis, DNA; D012984:Software