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
This docker image contains data that was submitted on or prior to 2024-12-31.
Available schemes found here: https://github.com/tseemann/mlst/tree/master/db/pubmlst
NOTE: This specific docker image also has 2 additional schemes that were not available in previous docker images:
- Serratia spp. https://pubmlst.org/organisms/serratia-spp
- Providencia spp. https://pubmlst.org/organisms/providencia-spp
These schemes can optionally be accessed using the mlst --scheme option with either serratia or providencia. mlst also has the ability to auto detect the scheme so it's not necessary to specify the scheme at runtime.
# 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 providencia psalmonis ranatipestifer rhodococcus
sagalactiae saureus sbsec scanis schromogenes sdysgalactiae senterica_achtman_2
sepidermidis serratia 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 xfastidiosamlst --nopath contigs.fasta > mlst-results.tsv