| name | cge-finders |
| description | Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for clinical/One-Health isolate typing and plasmid-borne AMR context — not community-wide dark-matter discovery. Child skills: plasmidfinder, resfinder, pointfinder, disinfinder, virulencefinder, mobileelementfinder, pmlst, staramr, abricate, mlst. Complements genomad, mob-suite, rgi, mobileog. Route via microbial-mining.
|
| license | MIT |
| category | orchestration |
| tags | ["CGE","Finder","PlasmidFinder","ResFinder","PointFinder","DisinFinder","VirulenceFinder","MobileElementFinder","pMLST","staramr","ABRicate","MLST","AMR","plasmid","MGE"] |
| stage | mining |
CGE Finders
CGE Finder tools (and close companions) screen draft assemblies against
curated marker databases for plasmids, acquired AMR, chromosomal AMR SNPs,
biocide genes, virulence genes, named MGEs, and sequence types. Best for
isolates / HQ MAGs — not a replacement for metagenome-native contig
classifiers (genomad) or CARD catalogues (rgi).
Web hub: https://www.genomicepidemiology.org/
Analytical thinking
| Claim | Prefer | Caution |
|---|
| Replicon / Inc-style plasmid typing | plasmidfinder | ≠ complete plasmid MAG |
| Plasmid scheme ST | pmlst | Must pick correct scheme |
| Chromosomal PubMLST ST | mlst | Not plasmid ST |
| Acquired AMR genes (ResFinder DB) | resfinder | ≠ CARD/rgi ontology |
| Chromosomal AMR point mutations | pointfinder (± resfinder -c) | Species-limited panels |
| Disinfectant / biocide genes | disinfinder (via ResFinder) | ≠ antibiotic MIC |
| Combined Res + Point + Plasmid | staramr | No VF / DisinFinder / pMLST |
| Multi-DB mass screen | abricate | No PointFinder phenotype maps |
| Virulence gene markers | virulencefinder (± abricate --db vfdb) | Narrow species DBs |
| Named IS / Tn / ICE / IME / … | mobileelementfinder | Complements isescan / mobileog |
| Meta plasmid/virus contigs | genomad · plasmaag | Different task |
| MOB / relaxase typing | mob-suite | Complements replicons |
| Broad resistome (CARD) | rgi (± deeparg) | Keep separate from ResFinder |
Hard rules:
- Pin software + database versions for every Finder / wrapper
- Prefer assembled contigs for isolate claims; state if using KMA on reads
- Do not equate Finder hits with phenotype or complete circular plasmids
- Keep ResFinder / DisinFinder / RGI-CARD tables separate unless cross-mapped
- Report chromosomal
mlst ST and plasmid pmlst ST as distinct claims
Decision tree
Isolate / CGE-style screen?
├─ Replicons → plasmidfinder
├─ Plasmid ST → pmlst
├─ Chromosomal ST → mlst
├─ Acquired AMR → resfinder
├─ Chromosomal AMR SNPs → pointfinder
├─ Biocide genes → disinfinder
├─ One report Res+Point+Plasmid → staramr
├─ Multi-DB BLAST screen → abricate
├─ Virulence markers → virulencefinder
├─ Named MGEs → mobileelementfinder
├─ Meta plasmid/virus contigs → genomad (± plasmaag)
├─ MOB / reconstruction → mob-suite
└─ CARD resistome → rgi
Related skills
plasmidfinder · pmlst · mlst · resfinder · pointfinder ·
disinfinder · virulencefinder · mobileelementfinder · staramr ·
abricate · genomad · mob-suite · plasmaag · mobileog · isescan ·
integronfinder · rgi · deeparg · microbial-mining · tool-selection
