Center for Genomic Epidemiology

To execute a sequence type prediction using the MLST web-server you need to follow the following 5 steps:

1. Choose the MLST profile for your organism

Use the drop down menu to select the MLST scheme. For most organisms only one MLST scheme is available.
For five organisms, two or three different MLST schemes are available:

• Acinetobacter baumannii (Acinetobacter baumannii#1 [1], Acinetobacter baumannii#2 [2]).
• Escherichia coli (Escherichia coli#1 [4], Escherichia coli#2 [5]).
• Leptospira spp., Leptospira spp.#2, Leptospira spp.#3
• Pasteurella multocida (Pasteurella multocida (RIRDC), Pasteurella multocida#2 (multihost)).
• Streptococcus thermophilus, Streptococcus thermophilus#2

2. Select minumin depth

Use the drop down menu to select the desired minimum depth. This is only relevant for raw read inputs and will not be used in case of assembled isolates. This will indicate the minimum required depth an allele will need to be considered a hit.

3. Select the type of your reads

See section 4 for more details on supported technologies and supported file formats.

4. Upload the file(s) of the isolate, or annotated genome, for which you want to know the sequence type.

The file to upload must contain assembled contigs, raw reads from the chosen sequencing technology or an annotated genome (among those shown in the mlst scheme drop down menu).

For preassembled partial or complete genomes, the input sequence must be in one-letter nucleotide code in a single FASTA file. The allowed alphabet (not case sensitive) is the following:

A C G T and N (unknown)

To input the sequences, upload a single FASTA file on your local disk by using the applet. First click on Isolate file then choose your file and click Open as shown in the image at the bottom of the page.

If your input consists of Raw Sequencing Reads, the MLST web-server will support FASTA and FASTQ files. Raw read from the following technologies is supported:

• Illumina Solexa single end reads
• Illumina Solexa paired end reads
• Roche 454 single end reads
• Roche 454 paired end reads
• Ion-torrent single end reads
• SOLiD single end reads
• SOLiD paired end reads
• SOLiD mate paired reads
• Pacific Biosciences (PacBio)
• Oxford Nanopore

Depending on the technology used, it may produce more than one raw read file. Therefore the webserver allows for multiple FASTA or FASTQ files to be uploaded. To input the sequences, upload the file(s) on your local disk by using the applet.

First click on Isolate file then choose your file(s) and click Open. If multiple files are to be uploaded for paired end reads you can select both files with Ctrl-Click (or Cmd-Click on Mac).

5. Submit the job

Click on the "Upload" button. The status of your job (either queued or running) will be displayed and constantly updated until it terminates and the server output page appears in your browser. You also have the option to input your email and be notified as soon as your the results are ready. The e-mail message will contain the URL under which the results are stored; they will remain on the server for one week for you to collect them

An overview of the upload