Fermented Foods Microbial Genomes Species-Representatives Functional Annotations

This repository contains raw files and results for functional annotations from 1236 species-representative bacterial genomes assembled from diverse fermented foods. The raw genome FASTA files and corresponding metadata area available in the Zenodo repository Fermented Foods Microbial Genomes Database. These files and results were produced as part of a collaboration with Tatta Bio to make these annotations available through their platform. This repository contains the following ZIP files and structures: species-reps-predicted-orfs.zip: For each genome is a .ffn, .faa, .gbk, and .gff file species-reps-main-results.zip: Output of the bac-mining workflow including summaries of each molecule type and counts across all genomes species-reps-summaries.zip: Output of running the create_genome_summaries.py helper script in the bac-mining repository for summarizing all annotation sources (smORFs, cleavage peptides, BGCs, and KofamScan annotations) in individual summary TSVs per genome This repository is slightly different from the data repository Predicted Biosynthetic Gene Clusters and Peptides from Fermented Food Microbial Genomes but contains some overlapping data. This repository contains all raw files and functional annotation information and summaries for 1236 species-representative genomes. These files were formatted specifically for the Tatta Bio platform. The other repository contains annotated summary files for cleavage peptides, smORFs, and BGCs predicted with antiSMASH for ~11,500 HQ genomes.