About
About
The characterization of microbial communities based on sequencing and analysis of their genetic information, also referred to as metagenomics, has become a popular approach; 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. Several approaches address 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 that gives 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 compared to existing tools.
Features
- Data and metadata capture
- Quality control reports
- analysis pipelines for taxonomic and functional analysis of raw reads
- metagenome (co-)assembly and taxonomic binning for MAG recovery
- de novo metatranscriptome assembly
- workflows for taxonomic and functional annotation of assemblies
- High-quality charts and interactive visualizations
- Statistics: PCA, PCoA, Rarefaction, ..
- Fragment recruitment
- Sequence export
- Custom pipeline support
Citation
MGX 2.0: Shotgun- and assembly-based metagenome and metatranscriptome analysis from a single source Sebastian Jaenicke, Sonja Diedrich, and Alexander Goesmann bioRxiv 2023.09.21.558800 DOI: 10.1101/2023.09.21.558800
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
Demo
If you want to try out MGX 2.0, we offer two public demonstration projects:
MGX2_Democontains sequence data from the black band disease study previously published by Sato et al. that was used as a demonstration example in the upcoming MGX 2.0 publication; ENA project accession PRJNA321354.
MGX2_TermiteGutwith metagenome and metatranscriptome date from the well-known termite gut study; ENA project accession PRJNA454696.
To access these example projects, download the MGX 2.0 application and log in with username mgxdemo and password mgxdemo. Please note that only read access is permitted here, i.e. you can explore all precomputed results and inspect the assemblies, but wont be able to initiate new analyses or delete existing data.
Funding
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.
Additional links
- Synthetic metagenomes used in the MGX manuscript are available from Zenodo
- Bioinformatics and Systems Biology at JLU Giessen
- Data privacy statement
- de.NBI - German network for bioinformatics infrastructure
- KEGG copyright request needed if you want to publish a KEGG pathway map created within MGX
