WGS Parameters of a locally create cgMLST Task Template
WGS Parameters of a Public cgMLST Task Template downloaded from the Task Template Sphere

Matching Tresholds for Scanning Targets

When WGS data is imported, SeqSphere+ scans the ref.-seqs. from the Task Template in the genome data using the integrated BLAST. If a unique hit exists and it reaches the the threshold that are specified here, the hit is imported as Target of the Task Entry.

Two thresholds are specified:

  • the required percental identity compared to the ref.-seq. of this target
  • the required percental aligned overlap compared to the full length of the ref.-seq. of this target

Doc-info.pngHint: For public Task Templates that were downloaded from the Task Template Sphere the thresholds are not editable.

Cluster-Alert Settings (only for cgMLST Task Templates)

Shows a summary of the pipeline results. The summary also shows if a Cluster Alert has occurred. This means that at least two Samples were found that have equal or more identical cgMLST than defined as Cluster Alert distance threshold in the WGS Parameters of the Task Template. For this comparison each newly imported Sample is compared against all Samples that currently exist in the database and using the same cgMLST scheme, even in other Projects.

  • Quality threshold of percental good cgMLST targets (default 90)
  • Distance threshold of maximum absolute different cgMLST targets, used to indicates epidemiological relationship between two Samples.

If the distance threshold is defined, the pipeline checks for Samples within this threshold after importing a new one, and reports the results in the Pipeline Report.

Doc-info.pngHint: For public cgMLST Task Templates that were downloaded from the Task Template Sphere the thresholds are not editable. The quality threshold defines if a sequence can be submitted to the nomenclature server. The distance threshold define the Cluster Type (CT) distance.