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
Available schemes found here: https://github.com/tseemann/mlst/tree/master/db/pubmlst
This docker image was built in January of 2024 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 yruckerimlst --nopath contigs.fasta > mlst-results.tsv