mob-suite

name	mob-suite
description	MOB-suite — plasmid reconstruction and typing from draft assemblies (replicon, relaxase/MOB type, mate-pair, transferability, mash clusters). Use for plasmid compatibility / MOB typing and plasmid contig binning beyond geNomad scores. Upstream: https://github.com/phac-nml/mob-suite. Route via microbial-mining; pair with genomad, plasmaag, mobileog, rgi.
license	MIT
category	analysis-tools
tags	["MOB-suite","plasmid","MOB","replicon","incompatibility","MGE","typing"]
upstream	https://github.com/phac-nml/mob-suite
stage	mining

MOB-suite

Upstream: phac-nml/mob-suite

Citation

Robertson, J. & Nash, J. H. E. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genom. 4, e000206 (2018). https://doi.org/10.1099/mgen.0.000206

See also docs/references.md.

Analytical thinking

MOB-suite types plasmids by replicon and MOB/relaxase markers and can reconstruct plasmid clusters from draft assemblies — useful for compatibility / transfer context (Inc/MOB-style interpretation as provided by the tool’s databases). Complements genomad (detection) and plasmaag (multi-sample plasmid MAGs).

Typing ≠ phenotypic incompatibility assay. Pin MOB-suite DB release.

How to run

# install mob_suite; download databases per upstream
mob_recon --infile assembly.fasta --outdir mob_out
mob_typer --infile plasmid.fasta --out mob_typer.tsv
# exact subcommands: follow installed version help

Decision tree

Plasmid typing / reconstruction?
├─ Contig plasmid/virus flags → genomad
├─ CGE replicon typing → plasmidfinder / staramr
├─ Replicon / MOB typing → mob-suite
├─ Multi-sample plasmid MAGs → plasmaag
├─ MGE protein functions → mobileog
└─ ARG on plasmids → resfinder / rgi ∩ mob-suite/genomad

Related skills

cge-finders · plasmidfinder · staramr · genomad · plasmaag · mobileog · integronfinder · rgi · resfinder · microbial-mining · tool-selection