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 -w80
aactinomycetemcomitans abaumannii abaumannii_2 achromobacter 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
cfreundii chlamydiales cmaltaromaticum cperfringens cronobacter csepticum
diphtheria_3 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
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 vvulnificusmlst --nopath contigs.fasta > mlst-results.tsv