Main tool : mlst
Additional tools:
- ncbi-blast+ 2.9.0
- perl 5.34.0
- any2fasta 0.4.2
Full documentation: https://github.com/tseemann/mlst
Scan contig files against PubMLST typing schemes
This docker image contains databases that were updated approximately in early December 2025 when version 2.25.0 of mlst was released.
Each subdirectory in /mlst-2.25.0/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
The Providencia spp. scheme (last updated 2025-12-11) was manually added to this docker image since it is not included by default with mlst v2.25.0. The FASTA files were downloaded from pubMLST.org and added to mlst's pubmlst database files & scheme. Users can either provide the argument --scheme providencia or allow for the auto-detection feature to detect the scheme automatically when typing Providencia genomes.
# 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
cdiphtheriae cfreundii chlamydiales cmaltaromaticum cperfringens cronobacter
csepticum diphtheria_3 dnodosus ecloacae ecoli ecoli_achtman_4 edwardsiella
efaecalis efaecium fpsychrophilum gallibacterium geotrichum hcinaedi
helicobacter hinfluenzae hparasuis hsuis kaerogenes kingella klebsiella
koxytoca leptospira leptospira_2 leptospira_3 lgarvieae liberibacter listeria_2
llactis_phage lsalivarius mabscessus magalactiae manserisalpingitidis mbovis
mbovis_2 mcanis mcaseolyticus mcatarrhalis_achtman_6 mflocculare mgallisepticum
mgallisepticum_2 mgenitalium mhaemolytica mhominis mhominis_3 mhyopneumoniae
mhyorhinis mhyosynoviae miowae 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 ranatipestifer rhodococcus
sagalactiae saureus sbsec scanis schromogenes sdysgalactiae senterica_achtman_2
sepidermidis serratia sgallolyticus shaemolyticus shewanella shominis siniae
sinorhizobium smaltophilia smitis spneumoniae spseudintermedius spyogenes ssuis
staphlugdunensis sthermophilus streptomyces streptothermophilus suberis
szooepidemicus taylorella tenacibaculum tpallidum tvaginalis ureaplasma
vcholerae vcholerae_2 vibrio vparahaemolyticus vtapetis vvulnificus wolbachia
xfastidiosa ypseudotuberculosis_achtman_3 yruckerimlst --nopath contigs.fasta > mlst-results.tsv