| name | rgi |
| description | Antibiotic resistance gene annotation against CARD. Use this skill when working with rgi: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/arpcard/rgi. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["AMR","CARD","resistance"] |
| upstream | https://github.com/arpcard/rgi |
RGI (CARD)
Upstream: arpcard/rgi · CARD database
Citation
Alcock, B. P. et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 51, D690–D699 (2023). https://doi.org/10.1093/nar/gkac920
See also docs/references.md.
Analytical thinking
RGI predicts AMR genes from proteins or contigs against CARD. Hits are
sequence homology / model matches — not phenotypic resistance, expression,
or clinical breakpoints.
Prefer protein mode on NR or MAG proteomes. Intersect with genomad/plasmaag
when claiming plasmid-borne AMR. Optional ML/complement: deeparg (different
model — do not merge unlabeled). Isolate CGE screens: resfinder / staramr
(ResFinder DB — keep separate from CARD).
How to run
rgi main -i proteins.faa -t protein -n 8 -a DIAMOND --clean \
-o result/card/protein
Key parameters
| Flag | Notes |
|---|
-t protein / contig | Protein preferred for catalogues |
-a DIAMOND | Speed |
| CARD version | Pin with RGI version |
Decision tree
Resistome claim?
├─ Homology to CARD → rgi
├─ CGE ResFinder DB (isolates) → resfinder / staramr
├─ Chromosomal AMR SNPs → pointfinder
├─ ML complement → deeparg (separate table)
├─ On plasmids? → intersect genomad / plasmaag / plasmidfinder
└─ Phenotype → needs experiments / MICs (out of scope)
Related skills
deeparg · resfinder · pointfinder · staramr · cge-finders ·
genomad · plasmaag · plasmidfinder · eggnog-mapper · prodigal ·
microbial-mining · visualization · tool-selection
