| name | plasmidfinder |
| description | PlasmidFinder — CGE in silico replicon / plasmid typing from assemblies or reads (BLAST/KMA vs PlasmidFinder DB). Use for Inc/replicon markers on isolates and HQ genomes. Upstream: https://github.com/genomicepidemiology/plasmidfinder. Route via cge-finders / microbial-mining; plasmid ST → pmlst; complement genomad, plasmaag, mob-suite.
|
| license | MIT |
| category | analysis-tools |
| tags | ["PlasmidFinder","CGE","plasmid","replicon","Inc","typing","MGE"] |
| upstream | https://github.com/genomicepidemiology/plasmidfinder |
| stage | mining |
PlasmidFinder
Upstream: genomicepidemiology/plasmidfinder ·
DB: plasmidfinder_db
Citation
Carattoli, A. et al. In Silico Detection and Typing of Plasmids using
PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob. Agents
Chemother. 58, 3895–3903 (2014). https://doi.org/10.1128/AAC.02412-14
See also docs/references.md and cge-finders.
Analytical thinking
PlasmidFinder matches replicon sequences (Inc/rep families as represented
in the CGE DB). A hit supports plasmid type presence, not a complete
circular plasmid or host linkage. Database historically strong for
Enterobacterales / selected Gram+ sets — weak for open environmental plasmidomes.
Prefer genomad / plasmaag for metagenomic plasmid contig discovery;
mob-suite for MOB/relaxase + reconstruction; PlasmidFinder for CGE-compatible
replicon typing on isolates.
How to run
python plasmidfinder.py -i assembly.fasta -o plasmidfinder_out \
-p /path/to/plasmidfinder_db
Exact flags vary by release — follow installed --help and pin DB commit/tag.
Decision tree
Plasmid claim?
├─ CGE replicon typing → plasmidfinder
├─ Plasmid scheme ST → pmlst
├─ Combined isolate AMR+plasmid report → staramr
├─ Multi-DB screen (incl. plasmidfinder DB) → abricate
├─ Contig plasmid/virus scores (meta) → genomad
├─ Plasmid MAG recovery → plasmaag
├─ MOB / relaxase typing → mob-suite
└─ ARG on plasmids → resfinder / rgi ∩ plasmidfinder/genomad
Related skills
cge-finders · pmlst · mlst · staramr · abricate · resfinder ·
mob-suite · genomad · plasmaag · mobileelementfinder · rgi ·
microbial-mining · tool-selection
