MIMOSA2 Reference Data Downloads

MIMOSA2 can use various types of reference data to construct metabolic models from a set of microbiome data. A subset of these are available for download below. The methods used to generate these files are described in the MIMOSA2 manuscript. Scripts to re-generate these files can be found in the “scripts” directory of the MIMOSA2 app GitHub repository.

Download all files needed for a specific workflow

See the R package tutorial for an overview of all workflows.

• 16S rRNA ASVs to EMBL_GEMS
• Greengenes or SILVA OTUs to EMBL_GEMs
• 16S rRNA ASVs to AGORA
• Greengenes or SILVA OTUs to AGORA
• 16S rRNA ASVs to KEGG - see Note
• Greengenes OTUs to KEGG - see Note
• Metagenomes to KEGG - see Note

Note: To use a KEGG-based workflow, you must have a KEGG license to download the necessary files, or you can run your analysis using the web app. The specific files and their setup are described in the R package tutorial.

You can also download freely available data for a particular workflow with the download_reference_data function in MIMOSA2 (see the R package tutorial).

If these links don’t work, try these backup links to access the EMBL_GEMS and AGORA databases.