VAMPS : a website for visualization and analysis of microbial population structures
Huse, Susan M.
Mark Welch, David B.
Morrison, Hilary G.
Eren, A. Murat
Sogin, Mitchell L.
MetadataShow full item record
KeywordMicrobiome; Microbial ecology; Microbial diversity; Data visualization; Website; Bacteria; SSU rRNA; Next-generation sequencing
The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Tactical decisions for changeable cuttlefish camouflage : visual cues for choosing masquerade are relevant from a greater distance than visual cues used for background matching Buresch, Kendra C.; Ulmer, Kimberly M.; Cramer, Corinne; McAnulty, Sarah; Davison, William; Mathger, Lydia M.; Hanlon, Roger T. (Marine Biological Laboratory, 2015-10-01)Cuttlefish use multiple camouflage tactics to evade their predators. Two common tactics are background matching (resembling the background to hinder detection) and masquerade (resembling an uninteresting or inanimate object ...
Lerner, Steven A. (Woods Hole Oceanographic Institution, 1999-08)Visual is a visualization system used to access and analyze high-volume multi-sensor data collected from remotely operated underwater vehicles. Since 1991, scientists have used Visual for scientific visualization and ...