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

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

doi:10.1093/bioinformatics/btu590

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

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

Authors

Mick Watson¹, Marian Thomson¹, Judith Risse¹, Richard Talbot¹, Javier Santoyo-Lopez¹, Karim Gharbi¹, Mark Blaxter¹

Affiliation

¹ Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG and Edinburgh Genomics, Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3JT, UK.

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/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Nanopores*
Sequence Analysis, DNA / methods*
Sequence Analysis, DNA / standards
Software*

Abstract

Publication types

MeSH terms

Grants and funding