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Bioinformatics Advance Access published online on January 25, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp017
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic data.context

Olivier Martin 1,*, Armand Valsesia 1,2,*, Amalio Telenti 3, Ioannis Xenarios 1 and Brian J. Stevenson 1,2,{ddagger}

1Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
2Ludwig Institute for Cancer Research, 1015 Lausanne, Switzerland
3Institute of Microbiology, University Hospital, University of Lausanne, 1011 Lausanne, Switzerland

{ddagger}To whom correspondence should be addressed. Dr.Brian J. Stevenson, E-mail: brian.stevenson{at}licr.org


  Abstract

Summary: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in a genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapmapHapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It offers a scalable visualization framework for a wide range of ‘omics’ dataIt implements an efficient cache system and allows the display of several, very large-scale genomic datasets.

Availability: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the Source-Forge repository: https://sourceforge.net/projects/associationview/. This also includes Java webstart, documentation and example datafiles.

Contact: brian.stevenson@licr.org

Associate Editor Prof. John Quackenbush

* These authors contributed equally to this work.

Received on September 16, 2008; revised on December 16, 2008; accepted on January 5, 2009

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