pku-embl/metagenomics-skills/cge-finders

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

Hard rules:

1. Pin software + database versions for every Finder / wrapper
2. Prefer assembled contigs for isolate claims; state if using KMA on reads
3. Do not equate Finder hits with phenotype or complete circular plasmids
4. Keep ResFinder / DisinFinder / RGI-CARD tables separate unless cross-mapped
5. Report chromosomal mlst ST and plasmid pmlst ST as distinct claims

Required inputs and delivery contract

Require stable isolate/genome IDs, assembly quality, organism assignment when a species-specific mutation panel is requested, exact software/database releases, and predeclared identity/coverage rules. Deliver separate raw and interpreted tables for acquired genes, point mutations, replicons, plasmid ST, chromosomal ST, virulence markers, biocide genes, and named MGEs; include no-hit and failed samples.

Cross-map databases only through a documented ontology table. Preserve coordinates and contig context so plasmid/MGE support can be graded separately from gene detection. Any phenotype field must identify the tool/database rule and remain a prediction unless matched to laboratory susceptibility testing.

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