title: The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.
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.
authors: Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors: Kevin
authors: K
authors: Riehle
authors: Cristian
authors: C
authors: Coarfa
authors: Andrew
authors: A
authors: Jackson
authors: Jun
authors: J
authors: Ma
authors: Arpit
authors: A
authors: Tandon
authors: Sameer
authors: S
authors: Paithankar
authors: Sriram
authors: S
authors: Raghuraman
authors: Toni-Ann
authors: TA
authors: Mistretta
authors: Delphine
authors: D
authors: Saulnier
authors: Sabeen
authors: S
authors: Raza
authors: Maria Alejandra
authors: MA
authors: Diaz
authors: Robert
authors: R
authors: Shulman
authors: Kjersti
authors: K
authors: Aagaard
authors: James
authors: J
authors: Versalovic
authors: Aleksandar
authors: A
authors: Milosavljevic
mesh_terms: D002648:Child; D019295:Computational Biology; D041981:Gastrointestinal Tract / Q000382:microbiology; D006801:Humans; D043183:Irritable Bowel Syndrome / Q000382:microbiology; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D009765:Obesity / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S