resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing微生物资源和成本序列分析评估使用虚拟机和云计算.pdfVIP

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing 1,2 1 1 1 1 Samuel V. Angiuoli *, James R. White , Malcolm Matalka , Owen White , W. Florian Fricke * 1 Institute for Genome Sciences (IGS), University of Maryland Baltimore, Baltimore, Maryland, United States of America, 2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America Abstract Background: The widespread popularity of genomic applications is threatened by the ‘‘bioinformatics bottleneck’’ resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly. Results: We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes