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 md5:e3e62b305e64b27da7b80655d7f92f2c 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 md5:cbcc9aa1a28a5bd5f6661f832d27bcbf 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 md5:2a49534b52169daa4f96157b15d1b01c 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 md5:75c435a69b183ea23aa58d43c1e051ba 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 md5:9e3f7a84fe7409ef0282ca5424797976 A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.