cgMLST.org Nomenclature Server

The cgMLST.org Nomenclature Server (www.cgMLST.org) provides a global nomenclature for stable public cgMLST schemes, i.e. for Task Templates that were downloaded from the Task Template Sphere. In contrast to a [Consortium Server], epi data of samples cannot be submitted to cgMLST.org.

Important: If no submission of any data, even allele data, is wanted or allowed, then only local Task Templates must be used. Samples that are using only local Task Templates will and cannot be submitted to cgMLST.org. Local Task Templates can be defined using the cgMLST Target Definer, or by converting public Task Templates into local ones.

Submission of Alleles

When Samples are processed for a downloaded Task Template, the new alleles are by default automatically submitted to and stored at cgMLST.org. The cgMLST.org Nomenclature Server assigns new global allele type numbers to the alleles. The allelic profile is not stored at cgMLST.org during allele submission.

The automatic allele submission can be disabled in the in the client settings, by using the menu item Options | Preferences, and selecting the the item Online Connection | Allele Submission to cgMLST.org. However, if a Sample has new alleles that are not known at cgMLST.org, the new alleles are treated as missing data in the distance calculation (e.g., in Comparison Table).

Submission of Allelic Profiles

For samples that do not belong to an existing Complex Type (CT), it is required to submit the allelic profile to define a new CT. The allelic profile of the new CT will be stored on cgMLST.org. No epi data or submitter data of the sample will be stored on cgMLST.org. Submission to cgMLST.org is only possible if the Sample has in the cgMLST scheme at least 90% of good targets (i.e., targets passed the QC procedure and have therefore a green or yellow smiley).

The automatic submission of allelic profiles can be configured in a pipeline script.

When Samples were loaded into workspace, the right-click menu function Submit Allelic Profile to cgMLST.org Nomenclature Server can be used to submit the allelic proflie and assign CTs for those samples.