Nagpal, S.; Haque, M.M.; Mande, S.S. ReFDash - A Repository of Functional Dashboards providing comprehensive functional insights inferred from 16S microbiome data sets. Preprints2019, 2019090070. https://doi.org/10.20944/preprints201909.0070.v1
APA Style
Nagpal, S., Haque, M.M., & Mande, S.S. (2019). <b>ReFDash - </b>A <strong>Re</strong>pository of <strong>F</strong>unctional <strong>Dash</strong>boards providing comprehensive functional insights inferred from 16S microbiome data sets. Preprints. https://doi.org/10.20944/preprints201909.0070.v1
Chicago/Turabian Style
Nagpal, S., Mohammed Monzoorul Haque and Sharmila S. Mande. 2019 "<b>ReFDash - </b>A <strong>Re</strong>pository of <strong>F</strong>unctional <strong>Dash</strong>boards providing comprehensive functional insights inferred from 16S microbiome data sets" Preprints. https://doi.org/10.20944/preprints201909.0070.v1
Abstract
Motivation: 16S rRNA gene amplicon based sequencing has significantly expanded the scope of metagenomics research by enabling microbial community analyses in a cost-effective manner. The possibility to infer functional potential of a microbiome through amplicon sequencing derived taxonomic abundance profiles has further strengthened the utility of 16S sequencing. In fact, a surge in 'inferred function metagenomic analysis' has recently taken place, wherein most 16S microbiome studies include inferred functional insights in addition to taxonomic characterization. Tools like PICRUSt, Tax4Fun, Vikodak and iVikodak have significantly eased the process of inferring function potential of a microbiome using the taxonomic abundance profile. A platform that can enable hosting of inferred function 'metagenomic studies' with comprehensive metadata driven search utilities (of a typical database), coupled with on-the-fly comparative analytics between studies of interest, can be a major improvement to the state of art. ReFDash represents an effort in the proposed direction. Methods: This work introduces ReFDash - a Repository of Functional Dashboards. ReFDash, developed as a significant extension of iVikodak (function inference tool), provides three broad unique offerings in inferred function space - (i) a platform that hosts a database of inferred function data being continously updated using public 16S metagenomic studies (ii) a tool to search studies of interest and compare upto three metagenomic environments on the fly (iii) a community initiative wherein users can contribute their own inferred function data to the platform. ReFDash therefore provides a first-of-its-kind community-driven frame-work for scientific collaboration, data analytics, and sharing in this area of microbiome research. Results: Overall, the ReFDash database is aimed at compiling together a global ensemble of 16S-derived Functional Metagenomics projects. ReFDash currently hosts close to 50 ready-to-use, re-analyzable functional dashboards representing data from approximately 18,000 microbiome samples sourced from various published studies. Each entry also provides direct downloadable links to associated taxonomic files and metadata employed for analysis. Conclusion: The vision behind ReFDash is creation of a framework, wherein users can not only analyze their microbiome datasets in functional terms, but also contribute towards building an information base by submitting their functional analyses to ReFDash database. ReFDash web-server may be freely accessed at https://web.rniapps.net/iVikodak/refdash/
Biology and Life Sciences, Immunology and Microbiology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
