Task Procedure of a locally created cgMLST Task Template
Task Procedure of a public cgMLST Task Template downloaded from the Task Template Sphere

Target Scan Procedure Details

When WGS data is imported, SeqSphere+ scans the data for the target ref.-seqs. from the Task Template (using the integrated BLAST). If the scan finds a unique hit for a target, that reaches the thresholds that are specified here, this hit is imported as Target of the Task Entry.

The following parameters can be specified:

  • Required identity to ref.-seq. (default for cgMLST: 90%)
Defines the required percental identity of the BLAST hit compared to the ref.-seq. of this target.
  • Required perc. aligned to ref.-seq. (default for cgMLST: 100%)
Defines the required percental aligned overlap compared to the full length of the ref.-seq. of this target.
  • Scan for allele library sequences if ref.-seq. not found or not defined (default for cgMLST: disabled)
This option can be enabled to scan not only for the ref.-seq. of a target, but for all allele that already exist in the allele library for this target.
  • Force using best match if multiple matches found within the thresholds (default for cgMLST: disabled)
By default, only unique hits are imported. If multiple different hits were found that all reach the defined thresholds, none is imported. If this option is enabled always the best match (by score) is imported.

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

Cluster-Alert Settings

Cluster-Alerts settings are only available for cgMLST Task Templates. It is used by a SeqSphere+ pipeline to automatically detect closely related Samples. For this comparison each newly imported Sample is compared against all Samples that currently exist in the database and using the same cgMLST scheme. If the pipeline founds existing Samples within these thresholds, they are reported in the Pipeline Report.

Two thresholds can be defined for the Cluster-Alert:

  • Cluster-Alert quality threshold (default for cgMLST: 90)
The quality threshold of percental good cgMLST targets that is required before the cluster-alert is performed.
  • Cluster-Alert distance threshold (default for cgMLST: empty)
The distance threshold of maximum absolute different cgMLST targets, that is used to indicates epidemiological relationship between two Samples. If the fields is empty, no Cluster-Alert checks are performed.
This threshold is also used as default for Similar Samples Search and MST clusters.

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

Other Settings

  • Keep read alignments of all targets (default for cgMLST: disabled)
By default, the read alignments for targets that pass the target QC procedure without errors or warnings are not kept. If this option is enabled, the read alignments are always kept.