Nephele: A cloud-based scientific computing platform for improved efficiency, standardization, and collaboration in microbiome data analysis

Authors

• N Weber
• M Coakley
• J Dommer
• A Gabrielian
• R Kaur
• L Kim
• A Levitsky
• D Liou
• P Macmenamin
• J Ning
• K Noble
• A Oler
• M Quiñones
• R Squires
• D Hurt

Abstract

Nephele is a cloud computing platform for microbiome research, aimed at providing scientists with a consistent, centralized, and collaborative environment for high-throughput metagenomics data analysis. Growing evidence supports a critical role for microbiota in human health and disease; 16S and whole genome sequence (WGS) analyses are critical to understanding this relationship, but analysis of large and complex datasets requires advanced computing infrastructure and sophisticated software that are inaccessible to many researchers. Nephele bridges this gap as an all-in-one portal to essential microbiome data and tools. The user-friendly, web-based interface directly links commonly-used metagenomics applications (QIIME, Mothur, BioBakery) to the Amazon Web Services (AWS) cloud. Preconfigured (but also customizable) pipelines lower the knowledge barrier for users who may be less familiar with command-line applications. Researchers can also seamlessly integrate public datasets into their analyses, including Human Microbiome Project (HMP) data, to compare against their own experimental sequence data. The on-demand, pay-per-use nature of cloud computing spares valuable funding and administrative resources for individual investigators and institutions by significantly reducing the cost of infrastructure procurement and maintenance. Open-source access to these tools and datasets encourages standardization of tools and methods, reproducibility of results, and extension of capabilities by the research community. By supporting greater adoption and improved efficiency in microbiome research, resources like Nephele can facilitate new discoveries that have the potential to transform medicine. NIH researchers and their collaborators are invited to request free AWS credits to explore the benefits of Nephele during its initial public release, commencing in Fall 2015.

Scientific Focus Area: Computational Biology

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