 WebMGA is a customizable web server that provides rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on a local computer cluster. It 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. and allows users to access it through web browsers or programming scripts to perform individual analysis or configure, and run customized pipelines. WebMGA is freely available at insert URL. This article was authored by Nioh Beifang, Fu Liming, Zhu Xunwei and others.