Process Genomes with Seed Only Scheme

  • Step 1: Create ad hoc cgMLST Task Template with the seed genome only and create a new project for it.
  • Step 2: Process genome data of all genomes into the new project.
  • Step 3: Delete insufficient genomes or mark them with a tag.

Find Targets to Exclude from Seed Only Scheme

Button16 Important.png Warning: For a large number of genomes this process requires a large amount of RAM (around 10 GB per 1000 genomes).

  • Step 1: Invoke in menu Tools | Sample QC Statistic
  • Step 2: Choose the project and the cgMLST task template.
  • Step 3: Select options Include Statistics per Target
  • Step 4: If necessary, define other criteria for the samples, e.g. not containing a tag that marks insufficient data.
  • Step 5: Press OK to continue.
  • Step 6: After statistic calculation has finished and results are shown.
  • Step 7: Go to tab 'Samples' > 'Summary' and check the Mean perc. good targets.
  • Step 8: Go to tab 'Targets' > 'Targets'
  • Step 9: Sort by Perc. Good in Samples
  • Step 10: Select all rows above a threshold in Perc. Good in Samples.
  • Step 11: Right-click on first column Target and invoke Copy Selected Values of Column to Clipboard

Evaluate Perc. Good Targets per Sample for Found Targets

Can be done multiple times for different thresholds. Multiple Sample QC Statistic windows can be left open at the same time.

  • Step 1: Invoke again in menu Tools | Sample QC Statistic
  • Step 2: Choose again the project and the cgMLST task template and continue with OK.
  • Step 3: Confirm dialog window with button Selected Targets.
  • Step 4: Paste into Filter the copied list of selected targets.
  • Step 5: Press Select All and confirm with OK.
  • Step 6: After statistic calculation has finished and results are shown.
  • Step 7: Go to tab 'Samples' > 'Summary' and check the Mean perc. good targets.

Exclude Found Targets from Final cgMLST Scheme

Button16 Important.png Important: Requires that the list of selected targets for the finally chosen threshold are in the clipboard.

  • Step 1: Invoke in menu Tools | cgMLST Target Definer
  • Step 2: Choose again the same seed genome.
  • Step 3: Go to tab Manually exclude genes and press Add Targets to Exclude
  • Step 4: In the upcoming dialog paste into Filter the copied list of selected targets.
  • Step 5: Press Select All.
  • Step 6: Clear the filter by pressing the button right of the filter text field.
  • Step 7: Press Invert Selection.
  • Step 8: Confirm with Move Targets to Accessory.
  • Step 9: Enter a descriptive reason for the exclusion of those genes for documentation.
  • Step 10: Press the Start button to start the core genome definer process.