MGX metagenome analysis platform

The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method. We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application. With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.


Project request

We operate and maintain two public MGX server instances hosted at the Bioinformatics and Systems Biology group at JLU Giessen and Center for Biotechnology, Bielefeld University. To obtain a protected project for analysis of own metagenome data, please get in touch with us and provide the following information:


The MGX user guide is available as an online HTML or PDF version.

MGX graphical user interface

The latest version of the MGX client application is provided as a platform-independent .zip archive from the releases page.


Flexible metagenome analysis using the MGX framework
Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye and Alexander Goesmann
Microbiome 2018 6:76
DOI: 10.1186/s40168-018-0460-1

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Funding for the operation and maintenance of MGX is provided by the German Federal Ministry of Education and Research (BMBF) project Bielefeld-Gießen Center for Microbial Bioinformatics - BiGi (grant 031A533) within the German Network for Bioinformatics Infrastructure (de.NBI).

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