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

BMC Bioinformatics

Software

Malcolm Matalka¹  Cesar Arze¹  James R White¹  David R Riley¹  Aaron Gussman¹  Kevin Galens¹  Mahesh Vangala¹  W Florian Fricke¹  Owen White¹  Samuel V Angiuoli² 

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

[2]Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, Maryland, USA

[3]Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA

关键词: Cloud Computing;    Virtual Machine;    Cloud Provider;    Master Node;    Cloud Computing Platform;   

DOI  :  10.1186/1471-2105-12-356

 received in 2011-06-07, accepted in 2011-08-30,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundNext-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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY   
© Angiuoli et al; licensee BioMed Central Ltd. 2011