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KEGG to R annotatOR (KEGG-R-ator)

Automate annotation and visualizations in R with KEGG.

Introduction

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

Contributors

Meagan Rubel (@marubel) Jesse Connell (@ressy) Louis Taylor (@louiejtaylor)