VAMPS: a website for visualization and analysis of microbial population structures

BMC Bioinformatics

Susan M Huse²  David B Mark Welch¹  Andy Voorhis¹  Anna Shipunova¹  Hilary G Morrison¹  A Murat Eren¹  Mitchell L Sogin¹ 

[1] Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA

[2] Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Campus Box G-E5, Providence, RI 02912, USA

关键词: Next-generation sequencing;    SSU rRNA;    Bacteria;    Website;    Data visualization;    Microbial diversity;    Microbial ecology;    Microbiome;   

Others  :  1087627
DOI  :  10.1186/1471-2105-15-41

 received in 2013-09-04, accepted in 2014-01-28,  发布年份 2014

【 摘 要 】

Background

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.

Results

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.

Conclusions

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.

【 授权许可】

   
2014 Huse et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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