Nephele 2.0: A robust online microbiome analysis platform

Authors

• M Quiñones
• L Kim
• P MacMenamin
• J Dommer
• P Subramanian
• C Shyu
• S Ezeji
• N Weber
• D Hurt

Abstract

Microbiome studies and their impact on health are enjoying increased awareness within the research community. Studies of the microbiome typically involve protocols such as whole metagenome shotgun sequencing (WGS) and sequencing of the 16S rRNA gene. Our team released the Nephele 1.0 platform in 2016 with the vision of providing access to microbiome data processing and analysis workflows to any researcher – especially those lacking advanced computing infrastructure and software. Nephele 1.0 has been used by over 700 microbiome researchers and students in over 80 countries. After evaluating users' feedback over two years, we identified significant hurdles including mapping file validation and the upload of large files via a browser. We also identified that a more robust infrastructure was of critical importance, allowing for faster development and troubleshooting of pipelines. The newly released Nephele 2.0. aims to reduce pipeline errors with a more efficient file upload and an interactive mapping file validation. This release also addresses a need for reduced computational time with faster AWS EC2 instances. Finally, Nephele 2.0, offers the following: 1) a new 16S survey pipeline based on the more refined DADA2 algorithm, in addition to the existing pipelines based on QIIME, mothur and Biobakery; 2) improved interactive visual outputs; 3) a more comprehensive user guide with video tutorials to assist the user with interpreting outputs and creating publication ready figures. The new infrastructure and features included in Nephele 2.0 offer microbiome researchers improved efficiency in data analysis and an overall better user experience.

Scientific Focus Area: Computational Biology

This page was last updated on Friday, March 26, 2021