| name | eggnog-mapper |
| description | Orthology-based functional annotation (COG/KEGG/CAZy via eggNOG). Use this skill when working with eggnog-mapper: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/eggnogdb/eggnog-mapper. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["annotation","orthology","function"] |
| upstream | https://github.com/eggnogdb/eggnog-mapper |
eggNOG-mapper
Upstream: eggnogdb/eggnog-mapper
Citation
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021). https://doi.org/10.1093/molbev/msab293
See also docs/references.md.
Analytical thinking
Annotate proteins from an NR gene catalogue or MAG proteomes via eggNOG
orthology (COG/KEGG/CAZy fields, etc.). DIAMOND mode is the common metagenome
default.
Combine with abundances carefully: sum TPM/counts of genes mapping to a KO/COG
only when the gene→function mapping is declared. Orthology hit ≠ experimental
function.
| vs other function layers | Notes |
|---|
humann | Read-level pathways (MetaCyc/UniRef) — different claim |
dram | Distilled MAG metabolism tables |
kegg | Direct KO maps (license) — may overlap fields |
How to run
emapper.py --data_dir ${db}/eggnog \
-i NR/protein.fa --cpu 16 -m diamond --override \
-o temp/eggnog/output
Key parameters
| Flag | Notes |
|---|
-m diamond | Typical metagenome speed/sensitivity balance |
--data_dir | Pin eggNOG DB release |
| Input | Proteins from prodigal / bakta |
Decision tree
Functional annotation need?
├─ Catalogue proteins → eggnog-mapper (+ salmon abundances)
├─ Read pathways → humann
├─ MAG metabolism distillate → dram
└─ AMR specifically → rgi
Methods caveats
- Pin emapper + eggNOG DB versions
- Do not label KEGG-like fields as full KEGG pathway proof without rules
Related skills
prodigal · salmon · diamond · dram · kegg · rgi · visualization ·
tool-selection
