Ontology highlight
ABSTRACT: Background
Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings.Methods
To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection.Results
We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome.Conclusions
By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.
SUBMITTER: Riehle K
PROVIDER: S-EPMC3426808 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Riehle Kevin K Coarfa Cristian C Jackson Andrew A Ma Jun J Tandon Arpit A Paithankar Sameer S Raghuraman Sriram S Mistretta Toni-Ann TA Saulnier Delphine D Raza Sabeen S Diaz Maria Alejandra MA Shulman Robert R Aagaard Kjersti K Versalovic James J Milosavljevic Aleksandar A
BMC bioinformatics 20120824
<h4>Background</h4>Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings.<h4>Methods</h4>To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the ...[more]