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:
Hint: 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.
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.
Hint: 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.