Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Software

Web-based visual analysis for high-throughput genomics

Jeremy Goecks12, Carl Eberhard12, Tomithy Too3, The Galaxy Team14, Anton Nekrutenko4 and James Taylor12*

Author Affiliations

1 Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA

2 Department of Mathematics and Computer Science, Emory University, 400 Downman Dr., Atlanta, GA 30322, USA

3 Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore

4 Center for Comparative Genomics and Bioinformatics, Penn State University, 505 Wartik Lab, University Park, PA 16802, USA

For all author emails, please log on.

BMC Genomics 2013, 14:397  doi:10.1186/1471-2164-14-397

Published: 13 June 2013

Abstract

Background

Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues.

Results

We have created a platform that simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org webcite) genomics workbench, making it easy to integrate new visual applications into Galaxy.

Conclusions

Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments.

Keywords:
Visualization; Visual analysis; Galaxy; Genome browser; Circos; Phylogenetic tree