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mlst container

Main tool : mlst

Additional tools:

  • ncbi-blast+ 2.9.0
  • perl 5.30.0
  • any2fasta 0.4.2

Full documentation: https://github.com/tseemann/mlst

Scan contig files against PubMLST typing schemes

pubMLST databases

Available schemes found here: https://github.com/tseemann/mlst/tree/master/db/pubmlst

This docker image was built in August of 2023 and databases were updated during the docker image build process. See Dockerfile for update commands.

# 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 
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 hcinaedi helicobacter hinfluenzae hparasuis hsuis 
kaerogenes kingella klebsiella koxytoca leptospira leptospira_2 leptospira_3 
liberibacter listeria_2 llactis_phage lsalivarius mabscessus magalactiae 
manserisalpingitidis mbovis_2 mcanis mcaseolyticus mcatarrhalis_achtman_6 
mflocculare mgallisepticum mgallisepticum_2 mhaemolytica mhominis_3 
mhyopneumoniae mhyorhinis miowae mplutonius mpneumoniae msciuri msynoviae 
mycobacteria_2 neisseria oralstrep orhinotracheale otsutsugamushi pacnes_3 
paeruginosa pdamselae pfluorescens pgingivalis plarvae pmultocida pmultocida_2 
ppentosaceus pputida psalmonis ranatipestifer rhodococcus sagalactiae saureus 
sbsec scanis schromogenes sdysgalactiae senterica_achtman_2 sepidermidis 
sgallolyticus shaemolyticus shewanella shominis sinorhizobium smaltophilia 
spneumoniae spseudintermedius spyogenes ssuis staphlugdunensis sthermophilus 
streptomyces streptothermophilus suberis szooepidemicus taylorella 
tenacibaculum tpallidum ureaplasma vcholerae vcholerae_2 vibrio 
vparahaemolyticus vtapetis vvulnificus wolbachia xfastidiosa 
ypseudotuberculosis_achtman_3 yruckeri

Example Usage

mlst --nopath contigs.fasta > mlst-results.tsv