microbetag : building a thorough database of genome-scale KO annotations

In this repository we keep internal data for the microbetag microbial co-occurrence network annotator.

microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file. 

gtdb_modelseed_gems.zip

for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions

gtdb_kofam_scan_per_module.tar.gz

all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. 

updated_seedsets_of_interest.pckl

A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        SeedSet373.172    [cpd00891, cpd00136, cpd00199, cpd01772, cpd00...397278.5   [cpd00891, cpd00136, cpd01772, cpd02698, cpd08...

updated_non_seedsets_of_interest.pckl

A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        NonSeedSet64187.548   [cpd00508, cpd00869, cpd00774, cpd03830, cpd00...74426.1719  [cpd00204, cpd00447, cpd20171, cpd03470, cpd00...

phen_classes.zip

A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.