| name | staramr |
| description | staramr — scan assemblies against ResFinder, PointFinder, and PlasmidFinder databases in one report (PHAC-NML). Use for isolate AMR + plasmid replicon summaries when you want CGE DBs without running each Finder separately. Upstream: https://github.com/phac-nml/staramr. Route via cge-finders / microbial-mining; CARD catalogues still via rgi.
|
| license | MIT |
| category | analysis-tools |
| tags | ["staramr","CGE","ResFinder","PointFinder","PlasmidFinder","AMR","plasmid"] |
| upstream | https://github.com/phac-nml/staramr |
| stage | mining |
staramr
Upstream: phac-nml/staramr
Citation
Bharat, A. et al. Correlation between Phenotypic and In Silico Detection of
Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.
Microorganisms 10, 292 (2022).
https://doi.org/10.3390/microorganisms10020292
Uses CGE databases — also cite ResFinder / PointFinder / PlasmidFinder papers
(see resfinder, pointfinder, plasmidfinder).
See also docs/references.md and cge-finders.
Analytical thinking
staramr is a convenience scanner over CGE ResFinder + PointFinder +
PlasmidFinder DBs with summary TSVs. Ideal for isolate batches and One-Health
surveillance pipelines. Still genotype-level — phenotype concordance is
organism/drug dependent.
Does not replace VirulenceFinder or MobileElementFinder. Does not use
CARD; keep rgi separate. For PointFinder, set the correct
--pointfinder-organism.
How to run
mamba install -c bioconda -c conda-forge staramr
staramr db update
staramr search --pointfinder-organism salmonella \
-o staramr_out assembly.fasta
Decision tree
Need Res + Point + Plasmid in one pass?
├─ Yes (isolates) → staramr
├─ Only acquired AMR CLI → resfinder
├─ Only replicons → plasmidfinder
├─ Virulence / named MGEs → virulencefinder / mobileelementfinder
└─ CARD meta catalogue → rgi
Related skills
cge-finders · resfinder · pointfinder · plasmidfinder ·
virulencefinder · mobileelementfinder · rgi · mob-suite · genomad ·
microbial-mining · tool-selection
