 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 is freely available at, insert URL. This article was authored by Niu Beifang, Fu Liming, Zhu Zhengwei and others.