| name | pmlst |
| description | pMLST — plasmid multilocus sequence typing from assemblies or reads using CGE / PubMLST plasmid schemes (IncI1, IncF, IncHI2, …). Use after PlasmidFinder replicon hits when a scheme ST is needed. Upstream: https://github.com/ssi-dk/pmlst (pmlst_ssi). Route via cge-finders / plasmidfinder / microbial-mining; chromosomal ST → mlst.
|
| license | MIT |
| category | analysis-tools |
| tags | ["pMLST","plasmid","MLST","CGE","typing","Inc","PubMLST"] |
| upstream | https://github.com/ssi-dk/pmlst |
| stage | mining |
pMLST
Upstream: ssi-dk/pmlst ·
PyPI/bioconda: pmlst_ssi · CGE service historically at genomicepidemiology.org
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, plasmidfinder, and
cge-finders.
Analytical thinking
pMLST assigns a plasmid sequence type for a chosen scheme after alleles
are called. Requires selecting the correct scheme (e.g. IncI1, IncF RST, …) —
wrong scheme → nonsense ST. Incomplete draft plasmids may yield partial
allelic profiles.
Typical order: plasmidfinder (replicon) → pmlst (scheme ST) → optional
mob-suite (MOB/reconstruction). Chromosomal isolate ST is mlst, not pMLST.
How to run
mamba install -c bioconda -c conda-forge pmlst_ssi
pmlst -i assembly.fasta -o pmlst_out -s IncI1
Pin software + scheme/database versions; report the scheme name with every ST.
Decision tree
Plasmid typing depth?
├─ Replicon only → plasmidfinder / staramr
├─ Plasmid ST (scheme) → pmlst
├─ Chromosomal ST → mlst
├─ MOB / reconstruction → mob-suite
└─ Meta plasmid contigs → genomad / plasmaag
Related skills
cge-finders · plasmidfinder · mlst · mob-suite · staramr ·
genomad · plasmaag · abricate · microbial-mining · tool-selection
