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microbetag: microbetagDB

microbetag is a software ecosystem for annotating microbial co-occurrence networks.

In this repository you may find:

  • in the current develop branch, the precalculation steps/scripts to build microbetagDB
  • in the preprocess branch, the microbetag-preprocessing stand-alone tool, provided as a Docker image
  • in the user-bins branch, a stand-alone version of microbetag to use with custom genomes, instead of mapping taxa to the GTDB representative genomes, provided as a Docker image too
  • in the gh-pages branch, we build the microbetag documentation page

For tutorials on how to use the different parts of the microbetag software ecosystem, please go through our documentation website.

microbetagDB

In the develop branch of this repo, you may find how we came up with the microbetagDB.

microbetagDB consists of 34,608 high-quality Genome Taxonomy DataBase genomes, along with their corresponding KEGG annotations and genome-scale metabolic reconstructions. Seed sets (externally acquired compounds) were retrieved from the latter, supporting the prediction of over 1 billion potential pairwise metabolic interactions. Relying on KEGG MODULE definitions, 342,000 unique pathway complements were identified based on pairwise overlaps between the annotated genomes. In addition, 33 phenotypic traits (e.g., pH optima, oxygen tolerance etc.) were predicted for the annotated genomes and incorporated in microbetagDB.

microbetag maps node taxonomies to their closest genome in microbetagDB and annotates them with phenotypic traits and functional potential derived from the literature. Edges are then annotated with pathway complements and seed complementarities that may represent cross-feeding relationships.

Graphical User Interphase (GUI)

To visualise microbetag-annotated networks but also to perform microbetag for simple cases without any need of running something locally, we provide a Cytoscape app.

The source code for the microbetag GUI can be found here.

Contact

For hints on how to use microbetag, ideas for new features and bug reports find us on out Matrix space. If you do not have a Matrix account, it’s only two clicks away! For more, you may check here.

Cite

In prep.

Funding

This project is funded by an EMBO Short-Term Fellowship and the 3D’omics Horizon project (101000309).

License

microbetag is under GNU General Public License v3.0. For third-party components separate licenses apply. The MGG CytoscapeApp is under Apache License, Version 2.0.