All MLST schema that are public available at can be directly downloaded through SeqSphere, using "Create Task Template by Predefined MLST Scheme" when creating a new Task Template. For non-public schemes, a Task Template can also be created from profile and allele library files.

Creating such a Task Template requires that you have a single FASTA file for each locus of the MLST, and a CSV file that contains the allelic profiles of the STs.

The names of the allelic library files will be the names of the targets in the Task Template. If the allelic profiles of the STs are only available in Excel file format (xls/xlsx), then they must be converted to CSV before they can be imported into SeqSphere+.

Creating the Task Template

  • Step 1: Invoke in the menu command Options | Task Templates.
  • Step 2: Press the button Create New.
  • Step 3: In the upcoming dialog choose Create Task Template for Whole Genome Sequencing Data.
  • Step 4: Choose Create Task Template by Allele Libraries.
  • Step 5: In the upcoming dialog enter a Name, the Genus and the Species for your Task Template.
  • Step 6: Choose in the field Application the value Typing.
  • Step 7: Press the button Import Allele Libraries.
  • Step 8: In the upcoming file dialog choose all the allele libraries as FASTA files. Each file represents one locus of the MLST.
  • Step 9: Confirm the upcoming "Import Allele Libraries" with OK.
  • Step 10: Press the button Next.
  • Step 11: The QC Procedure settings are shown. They can be left to default. Press the button Next.
  • Step 12: Finally press the button Finish to store the new Task Template.
  • Step 13: The new Task Template appears in the list of Task Templates and is still selected. Press the Edit button to open it again.
  • Step 14: Switch in the upcoming editor dialog to the tab Genotyping Libraries.
  • Step 15: Select the first row in the table (Type: Allele Typing), press the Delete button, and confirm to remove it.
  • Step 16: Now press the button Create New.
  • Step 17: In the upcoming dialog click on the option Add MLST Libraries.
  • Step 18: Next enter as Name "MLST".
  • Step 19: Switch to the tab Allele Libraries.
  • Step 20: Press the Button16-New.gif for the first target.
  • Step 21: In the upcoming dialog press the button Import From File and choose the allele library file (FASTA) of the first locus.
  • Step 22: Repeat step 20 and 21 for all targets.
  • Step 23: Switch to the tab Sequence Types, press the button Import From File and choose the CSV file that contains the allelic profiles for the STs (only CSV is supported here!).
  • Step 24: A preview dialog of the STs is shown. Click on the red headers of the table, and select the columns for the ST and for the loci in the table (the menu option Detect Mapping by Columns Headers can be used if the names are equal to the library file names.
  • Step 25: If the ST and all loci are mapped to columns, the dialog can be confirmed with OK.
  • Step 26: No press Finish to add the new Genotyping to the Task Template.
  • Step 27: Finally press OK to close the editor dialog, and Save Changes to store the Task Template.