MLST

What does it do?

The automator runs MLST analyses on provided SEQIDs. If the MLST database for the requested genus is not present on the NAS, or an update is requested, the automator downloads and prepares the database. It also runs GeneSeekr to perform MLST analyses. GeneSeekr MLST reports are uploaded and attached to the issue.

How do I use it?

Subject

In the Subject field, put mlst spelling counts, but case sensitivity doesn't.

Description

Include the genus on the first line organism=[name of organism]. Please note that both spelling AND case sensitivity are important. Here are the organisms currently available for this automator:

Full list of supported organisms

Achromobacter spp.
Acinetobacter baumannii#1
Acinetobacter baumannii#2
Aeromonas spp.
Aggregatibacter actinomycetemcomitans
Anaplasma phagocytophilum
Arcobacter spp.
Aspergillus fumigatus
Bacillus cereus
Bacillus licheniformis
Bacillus subtilis
Bacteroides fragilis
Bartonella bacilliformis
Bartonella henselae
Bartonella washoensis
Bordetella spp.
Borrelia spp.
Brachyspira hampsonii
Brachyspira hyodysenteriae
Brachyspira intermedia
Brachyspira pilosicoli
Brachyspira spp.
Brucella spp.
Burkholderia cepacia complex
Burkholderia pseudomallei
Campylobacter concisus/curvus
Campylobacter fetus
Campylobacter helveticus
Campylobacter hyointestinalis
Campylobacter insulaenigrae
Campylobacter jejuni
Campylobacter lanienae
Campylobacter lari
Campylobacter sputorum
Campylobacter upsaliensis
Candida albicans
Candida glabrata
Candida krusei
Candida tropicalis
Candidatus Liberibacter solanacearum
Carnobacterium maltaromaticum
Chlamydiales spp.
Citrobacter freundii
Clonorchis sinensis
Clostridioides difficile
Clostridium botulinum
Clostridium perfringens
Clostridium septicum
Corynebacterium diphtheriae
Cronobacter spp.
Cutibacterium acnes
Dichelobacter nodosus
Edwardsiella spp.
Enterobacter cloacae
Enterococcus faecalis
Enterococcus faecium
Escherichia coli#1
Escherichia coli#2
Flavobacterium psychrophilum
Gallibacterium anatis
Geotrichum spp.
Glaesserella parasuis
Haemophilus influenzae
Helicobacter cinaedi
Helicobacter pylori
Helicobacter suis
Kingella kingae
Klebsiella aerogenes
Klebsiella oxytoca
Klebsiella pneumoniae
Kudoa septempunctata
Lactobacillus salivarius
Lactococcus lactis bacteriophage
Leptospira spp.
Leptospira spp.#2
Leptospira spp.#3
Listeria monocytogenes
Macrococcus canis
Macrococcus caseolyticus
Mammaliicoccus sciuri
Mannheimia haemolytica
Melissococcus plutonius
Moraxella catarrhalis
Mycobacteria spp.
Mycobacteroides abscessus
Mycoplasma agalactiae
Mycoplasma anserisalpingitidis
Mycoplasma bovis
Mycoplasma flocculare
Mycoplasma gallisepticum#1
Mycoplasma gallisepticum#2
Mycoplasma hominis
Mycoplasma hyopneumoniae
Mycoplasma hyorhinis
Mycoplasma iowae
Mycoplasma pneumoniae
Mycoplasma synoviae
Neisseria spp.
Orientia tsutsugamushi
Ornithobacterium rhinotracheale
Paenibacillus larvae
Pasteurella multocida#1
Pasteurella multocida#2
Pediococcus pentosaceus
Photobacterium damselae
Piscirickettsia salmonis
Porphyromonas gingivalis
Pseudomonas aeruginosa
Pseudomonas fluorescens
Pseudomonas putida
Rhodococcus spp.
Riemerella anatipestifer
Salmonella enterica
Saprolegnia parasitica
Shewanella spp.
Sinorhizobium spp.
Staphylococcus aureus
Staphylococcus chromogenes
Staphylococcus epidermidis
Staphylococcus haemolyticus
Staphylococcus hominis
Staphylococcus lugdunensis
Staphylococcus pseudintermedius
Stenotrophomonas maltophilia
Streptococcus agalactiae
Streptococcus bovis/equinus complex (SBSEC)
Streptococcus canis
Streptococcus dysgalactiae equisimilis
Streptococcus gallolyticus
Streptococcus oralis
Streptococcus pneumoniae
Streptococcus pyogenes
Streptococcus suis
Streptococcus thermophilus
Streptococcus thermophilus#2
Streptococcus uberis
Streptococcus zooepidemicus
Streptomyces spp
Taylorella spp.
Tenacibaculum spp.
Treponema pallidum
Trichomonas vaginalis
Ureaplasma spp.
Vibrio cholerae
Vibrio cholerae#2
Vibrio parahaemolyticus
Vibrio spp.
Vibrio tapetis
Vibrio vulnificus
Wolbachia
Xylella fastidiosa
Yersinia pseudotuberculosis
Yersinia ruckeri

You can also choose to update the OLC database by entering update on the next line.

Then add the SEQID's on separate lines to match the rest of the document.

Note that FASTA files can also be attatched to the issue and be processed. This can used in addition to or instead of SEQIDs. However, there is a 5MB limit to the attatched file enforced by Redmine.

Example

For an example mlst see issue 34327 or issue 34328.

Interpreting Results

If submitted correctly you will recieve a zip folder named geneseekr_output_[issue num].zip that contains a excel sheet you can download.

How long does it take?

It should take a minute or two for the automator to run depending on whether the database needs to be installed/updated. Adding more sequences will scale up the time required.

What can go wrong?

A few things can go wrong with this process:

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.

2) Requested an unsupported organism. Please see the list of supported organisms above.

Version

The databases can be updated by including the update argument in the description.