ShortRead

a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

Morgan, Martin
Anders, Simon
Lawrence, Michael
Aboyoun, Patrick
Pagès, Hervé
Gentleman, Robert

¹Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
²European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK

Received on April 16, 2009; revised on June 23, 2009; accepted on July 15, 2009; Advance Access publication August 3, 2009

Associate Editor: Dmitrij Frishman

Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows.

Contact: [email protected]

^*To whom correspondence should be addressed.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Bioinformatics 25(19):p 2607-2608, October 1, 2009.

Summary

ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.