Email updates

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

Open Access Highly Accessed Software

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Samuel V Angiuoli12*, Malcolm Matalka1, Aaron Gussman1, Kevin Galens1, Mahesh Vangala1, David R Riley1, Cesar Arze1, James R White1, Owen White1 and W Florian Fricke1*

Author Affiliations

1 Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, Maryland, USA

2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA

For all author emails, please log on.

BMC Bioinformatics 2011, 12:356  doi:10.1186/1471-2105-12-356

Published: 30 August 2011

Abstract

Background

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.

Results

We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.

Conclusion

The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.