Yi Wang1,2,3, Ling Xu2,3, Yong Q Gu1, Devin Coleman-Derr2,3. 1. USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA. 2. Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 3. USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
Abstract
MOTIVATION: A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome. RESULTS: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome and provides a comparison of the relative abundance and diversity patterns between subsets of samples within a microbiome dataset. MetaCoMET provides an efficient and interactive graphical interface for analyzing each subset defined by the union or disjunction of groups within the Venn diagram, and includes a graphical taxonomy summary, alpha diversity metrics, Principal Coordinate analysis, abundance-based heatmaps, and a chart indicating the geographic distribution of each sample. AVAILABILITY AND IMPLEMENTATION: MetaCoMET is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/MetaCoMET or http://aegilops.wheat.ucdavis.edu/MetaCoMET CONTACT: devin.coleman-derr@ars.usda.govSupplementary information: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.
MOTIVATION: A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome. RESULTS: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome and provides a comparison of the relative abundance and diversity patterns between subsets of samples within a microbiome dataset. MetaCoMET provides an efficient and interactive graphical interface for analyzing each subset defined by the union or disjunction of groups within the Venn diagram, and includes a graphical taxonomy summary, alpha diversity metrics, Principal Coordinate analysis, abundance-based heatmaps, and a chart indicating the geographic distribution of each sample. AVAILABILITY AND IMPLEMENTATION: MetaCoMET is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/MetaCoMET or http://aegilops.wheat.ucdavis.edu/MetaCoMET CONTACT: devin.coleman-derr@ars.usda.govSupplementary information: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.
Authors: Grant T Kirker; Amy B Bishell; Michelle A Jusino; Jonathan M Palmer; William J Hickey; Daniel L Lindner Journal: Front Microbiol Date: 2017-10-18 Impact factor: 5.640
Authors: Torben Sølbeck Rasmussen; Liv de Vries; Witold Kot; Lars Hestbjerg Hansen; Josué L Castro-Mejía; Finn Kvist Vogensen; Axel Kornerup Hansen; Dennis Sandris Nielsen Journal: Viruses Date: 2019-05-13 Impact factor: 5.048
Authors: Colin P McNally; Alexander Eng; Cecilia Noecker; William C Gagne-Maynard; Elhanan Borenstein Journal: Front Microbiol Date: 2018-03-01 Impact factor: 5.640