MGnify

MGnify is a free resource for the archiving, analysis, visualisation, and discovery of metagenomic, metatranscriptomic, amplicon, and assembly datasets (Richardson et al 2023). It provides automated pipelines for analysing microbiome data, helping to determine the taxonomic diversity and functional and metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all the analysed public datasets in the repository. 

MGnify maintains an extensive collection of analysed microbiome datasets, processed using standardised pipelines and workflows. This enables contextual analysis alongside other studies from similar environments. MGnify is tightly integrated with ENA; raw metagenomic datasets are archived in ENA, where users can also submit their own data. MGnify analysis can then be requested for any suitable dataset in ENA – whether that be publicly available studies or a user’s own private data. In addition, when MGnify performs a metagenomic assembly, the resulting assemblies are archived back into ENA.

Alongside the standardised metagenome analysis pipelines, MGnify also provides the MGnify Proteins resource an annotated database of 3B protein sequences predicted from metagenomic assemblies – and the MGnify Genomes resource (Gurbich et al 2023) – a curated collection of biome-specific catalogues of annotated metagenome-assembled genomes (MAGs).

For a brief overview of MGnify and how you can use it in your research watch this recorded talk from Sandy Rogers, Senior software developer at EMBL-EBI.

The following pages offer practical material specifically designed for eDNA research to help you become familiar with using MGnify.