| 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
mob_recon --infile assembly.fasta --outdir mob_out
mob_typer --infile plasmid.fasta --out mob_typer.tsv
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
