Automated and portable sequence analysis from the desktop using cloud computing
Affordability of large-scale sequencing has decentralized genomic research, vastly increasing access and applications in clinical and public health settings. Coupled with this increase is an explosion of data that requires extensive bioinformatics analysis and access to compute resources. Cloud computing has the potential to make large-scale sequence analysis fast and easily accessible by providing compute resources on-demand over the Internet.
CloVR is a desktop application that integrates state-of-the-art genomic tools in a robust, user friendly, and fully automated software package with optional support for cloud computing platforms. CloVR currently bundles push-button pipelines for microbial genomics, including single-genome projects, 16S rRNA sequence analysis, and metagenomic sequencing projects. Additional pipelines for comparative genome analysis, prokaryotic and eukaryotic RNA-sequencing and viral genomics are planned.
CloVR is distributed as a portable virtual machine that is launched on a desktop or laptop under VMware or Virtualbox. Optionally, CloVR automatically manages additional resources on the cloud to perform large-scale sequence analysis. CloVR supports multiple cloud providers, including Amazon EC2, and academic clouds for research.
Project Publications
Angiuoli SV, White JR, Matalka M, White O, Fricke WF. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PloS One. 2011 Oct 19.
Angiuoli SV, Matalka M, Gussman G, Galens K, Vangala M, Riley DR, Arze C, White JR, White O and Fricke WF. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011 Aug;12:356.
White JR, Arze C, Matalka M, The CloVR Team, Angiuoli SV & Fricke WF. CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0. Nature Precedings. 05 April 2011.
White JR, Arze C, Matalka M, The CloVR Team, Angiuoli SV & Fricke WF. CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0. Nature Precedings. 05 April 2011.
Galens K, White JR, Arze C, Matalka M, Gwinn MG, The CloVR Team, Angiuoli SV & Fricke WF. CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0. Nature Precedings. 05 April 2011.
White JR, Matalka M, Fricke WF & Angiuoli SV. Cunningham: a BLAST Runtime Estimator. Nature Precedings. Jan 2011.
Research publications using CloVR
Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci USA. doi:10.1073/ pnas.1111712108, 2011 Nov 28.
Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, Leclerc JE, Ravel J, Cebula TA. Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. J Bacteriol. 2011 Jul;193(14):3556-68. Epub 2011 May 20.
Zan J, Fricke WF, Fuqua C, Ravel J, Hill R. Genome Sequence of Ruegeria sp. KLH11, a N-Acylhomoserine Lactone-Producing Bacterium Isolated from the Marine Sponge Mycale laxissima. J Bacteriol. 2011 Jul 8.
Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS. Bacterial community diversity and variation in spray water sources and the tomato fruit surface. BMC Microbiol. 2011 Apr 21;11:81. – In this publication, 16S rRNA analysis results generated with CloVR-16S are compared to those from other protocols.
