pmlst

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

# bioconda preferred
mamba install -c bioconda -c conda-forge pmlst_ssi
# select scheme per upstream docs / --help
pmlst -i assembly.fasta -o pmlst_out -s IncI1
# exact entrypoint/flags vary by packaging — follow installed help

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