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. 2015 Jan 1;31(1):114-5.
doi: 10.1093/bioinformatics/btu590. Epub 2014 Aug 29.

poRe: an R package for the visualization and analysis of nanopore sequencing data

Mick Watson  1 , Marian Thomson  1 , Judith Risse  1 , Richard Talbot  1 , Javier Santoyo-Lopez  1 , Karim Gharbi  1 , Mark Blaxter  1
Affiliations

poRe: an R package for the visualization and analysis of nanopore sequencing data

Mick Watson et al. Bioinformatics. .

Abstract

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/.

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Figures

Fig. 1.
Fig. 1.
An example output from the plot.squiggle function. Plotted are the events data extracted from a single read. The y-axis is the mean electronic signal reported for the pore, and the x-axis is time in seconds
See this image and copyright information in PMC

References

    1. R Core Team. R: A Language and Environment for Statistical Computing. 2014 R Foundation for Statistical Computing, Vienna, Austria.
    1. Bowers J, et al. Virtual terminator nucleotides for next-generation DNA sequencing. Nat. Methods. 2009;6:593–595. - PMC - PubMed
    1. Eid J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–138. - PubMed
    1. Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics. 2014 pii, btu555. - PMC - PubMed

Publication types