Main tool : mlst
Additional tools:
- ncbi-blast+ 2.17.0
- perl 5.34.0
- any2fasta 0.8.1
Full documentation: https://github.com/tseemann/mlst
Scan contig files against PubMLST typing schemes
This docker image contains databases that were updated approximately in late December 2025 when version 2.28.1 of mlst was released.
Each subdirectory in /mlst-{VERSION}/db/pubmlst/<scheme-name>/ contains a file database_version.txt that indicates the date that the specific database was last updated.
Available schemes found here: https://github.com/tseemann/mlst/tree/master/db/pubmlst
# sorted list of available mlst schemes
$ mlst --list 2>/dev/null | tr ' ' '\n' | sort | tr '\n' ' ' | fold -s -w80aactinomycetemcomitans abaumannii abaumannii_2 achromobacter actinobacillus aeromonas aparagallinarum aphagocytophilum arcobacter bbacilliformis bcc bcereus bfragilis bhenselae blicheniformis_14 bordetella_3 borrelia bpseudomallei brachyspira brachyspira_2 brachyspira_3 brachyspira_4 brachyspira_5 brucella bsubtilis bwashoensis campylobacter campylobacter_nonjejuni campylobacter_nonjejuni_2 campylobacter_nonjejuni_3 campylobacter_nonjejuni_4 campylobacter_nonjejuni_5 campylobacter_nonjejuni_6 campylobacter_nonjejuni_7 campylobacter_nonjejuni_8 campylobacter_nonjejuni_9 cbotulinum cdifficile cdiphtheriae cfreundii chlamydiales cmaltaromaticum cperfringens cronobacter csepticum dnodosus ecloacae ecoli ecoli_achtman_4 edwardsiella efaecalis efaecium fpsychrophilum gallibacterium geotrichum halobacteria hcinaedi helicobacter hinfluenzae hparasuis hsomni hsuis kaerogenes kingella klebsiella koxytoca leptospira leptospira_2 leptospira_3 lgarvieae liberibacter listeria_2 llactis_phage lsalivarius mabscessus magalactiae mamphoriforme manserisalpingitidis mbovis mbovis_2 mcanis mcaseolyticus mcatarrhalis_achtman_6 mflocculare mgallisepticum mgallisepticum_2 mgenitalium mhaemolytica mhominis mhominis_3 mhyopneumoniae mhyorhinis mhyosynoviae miowae morganella mplutonius mpneumoniae msciuri msynoviae mycobacteria_2 neisseria oralstrep orhinotracheale otsutsugamushi pacnes_3 paeruginosa pdamselae pfluorescens pgingivalis plarvae pmultocida pmultocida_2 ppentosaceus pputida proteus providencia psalmonis pstuartii ranatipestifer rhodococcus sagalactiae salmonella saureus sbsec scanis scapitis schromogenes sdysgalactiae senterica_achtman_2 sepidermidis serratia sgallolyticus shaemolyticus shewanella shominis siniae sinorhizobium smaltophilia smitis sparasuis spneumoniae spseudintermedius spyogenes ssuis staphlugdunensis sthermophilus streptomyces streptothermophilus suberis szooepidemicus taylorella tenacibaculum tpallidum tpyogenes tvaginalis ureaplasma vcholerae vcholerae_2 vibrio vparahaemolyticus vtapetis vvulnificus
## Example Usage
```bash
mlst --nopath contigs.fasta > mlst-results.tsv