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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke

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. More... »

PAGES

356

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-12-356

DOI

http://dx.doi.org/10.1186/1471-2105-12-356

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1026686709

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21878105


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Download the RDF metadata as:  json-ld nt turtle xml License info

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