MICOM model databases version 1

This repository includes pre-built model databases for the microbial community modeling tool MICOM (https://micom-dev.github.io/micom). All model databases will work with the MICOM python package or the MICOM Qiime 2 plugin (http://github.com/micom-dev/q2-micom).

The Zenodo release is built and versioned automatically from the the source repository at http://github.com/micom-dev/databases. Thus, all bug reports, requests, and comments should be made there.
Model databases are named with the following scheme:
SOURCE_SVER_TAXONOMY_RANK_VERSION.qza
where:

• SOURCE = source database for the models
• SVER = version of the source database
• TAXONOMY = the taxonomy naming scheme used
• RANK = the taxonomic rank models were collapsed on
• VERSION = the version of the built database

For all practical purposes the TAXONOMY should coincide with the taxonomic classification of your amplicons or genomes. For instance, if you used kraken2 and bracken2 you should use a model database with TAXONOMY = ncbi. Note that some taxonomy databases (GTDB, GreenGenes) prefix taxonomy identifiers with a rank indentifier like `s__Species`. Those are usually maintained in the databases here except for the NCBI Taxonomy which usually does not use those. You can verify taxon names using the manifests in the `release` section of http://github.com/micom-dev/databases .

For growth media that can be used with the model databases here please see the MICOM media repository at https://github.com/micom-dev/media.