KEGG to R annotatOR (KEGG-R-ator)
KEGG-R-ator is a Sunbeam extension written in snakemake that creates and aligns a DIAMOND-built database of metagenomic reads to KEGG, builds output files for KEGG enzymes, modules, and pathways, and visualizes the results. KEGG-R-ator uses conda to manage dependencies.
Specifically, KEGG-R-ator automates the following tasks:
- sbx_gene_clusters is used to make a blastdb from merged, paired-end reads using Diamond and a fasta file of reference sequences.
- R build of KEGG gene numbers to KEGG orthologs
- R build of KEGG orthologs to KEGG pathways in genes
- R build of KEGG enzymes from EC numbers in enzyme.list
- R build to KEGG modules from ko modules.list
KEGG-R-ator output can be used to generate heatmaps of differentially enriched pathways/enzymes/modules between groups: LEfSe