| name | mlst |
| description | mlst — chromosomal multilocus sequence typing of assemblies against PubMLST schemes (Torsten Seemann wrapper). Use for isolate / HQ-MAG species ST calling. Upstream: https://github.com/tseemann/mlst. Route via cge-finders / microbial-mining for isolate packages; plasmid ST → pmlst (different schemes).
|
| license | MIT |
| category | analysis-tools |
| tags | ["MLST","PubMLST","typing","isolate","ST","epidemiology"] |
| upstream | https://github.com/tseemann/mlst |
| stage | mining |
mlst
Upstream: tseemann/mlst · schemes from
PubMLST
Citation
Seemann, T. mlst: scan contig files against PubMLST typing schemes.
https://github.com/tseemann/mlst
Jolley, K. A., Bray, J. E. & Maiden, M. C. J. Open-access bacterial population
genomics: BIGSdb software, the PubMLST.org website and their applications.
Wellcome Open Res. 3, 124 (2018).
https://doi.org/10.12688/wellcomeopenres.14826.1
See also docs/references.md and pmlst.
Analytical thinking
Chromosomal MLST assigns a species-scheme sequence type from seven (or
scheme-defined) housekeeping loci. Auto-scheme detection can mis-assign on
novel/environmental genomes — verify species/--scheme. Novel alleles yield
incomplete STs.
Not plasmid typing (pmlst) and not ANI taxonomy (gtdbtk / skani).
Use with CGE Finders for One-Health isolate reports: species ST + resistome +
plasmids.
How to run
mamba install -c bioconda -c conda-forge mlst
mlst assembly.fasta > mlst.tsv
mlst --scheme ecoli assembly.fasta
Pin mlst version and PubMLST scheme download date.
Decision tree
Sequence type needed?
├─ Chromosomal PubMLST ST → mlst
├─ Plasmid scheme ST → pmlst
├─ Species/taxonomy for MAGs → gtdbtk
└─ AMR / plasmids / virulence → cge-finders / abricate / rgi
Related skills
pmlst · cge-finders · abricate · staramr · plasmidfinder ·
gtdbtk · microbial-mining · tool-selection
