Introduction

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/npReaderm.cao1@uq.edu.au or l.coin@imb.uq.edu.au.

Publications

  1. Realtime analysis and visualization of MinION sequencing data with npReader.
    Cite this
    Cao MD, Ganesamoorthy D, Cooper MA, Coin LJ, 2016-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Minh Duc Cao
    Developer

    Institute for Molecular Bioscience, The University of Queensland, Australia

  2. Devika Ganesamoorthy
    Developer

    Institute for Molecular Bioscience, The University of Queensland, Australia

  3. Matthew A Cooper
    Developer

    Institute for Molecular Bioscience, The University of Queensland, Australia

  4. Lachlan J M Coin
    Investigator

    Institute for Molecular Bioscience, The University of Queensland, Australia

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Summary
AccessionBT002127
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionAustralia
Submitted ByLachlan J M Coin