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WebMGA: a customizable web server for fast metagenomic sequence analysis

Sitao Wu, Zhengwei Zhu, Liming Fu, Beifang Niu and Weizhong Li*

Author Affiliations

Center for Research in Biological Systems, University of California San Diego, La Jolla, California 92093, USA

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BMC Genomics 2011, 12:444  doi:10.1186/1471-2164-12-444

Published: 7 September 2011



The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc.


We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at webcite.


WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.