Analysis Configuration Template

Analysis Configuration Template is a template containing configuration/settings for a secondary analysis to allow planning a run on Clarity LIMS. Analysis Configuration Templates created on BaseSpace Sequence Hub can be retrieved and used in a workflow on Clarity Lab Information Management System (LIMS).

To use Analysis Configuration Template, please turn on the Advanced LIMS Run Planning from the User Account Settings page (Note that only Workgroup owner has the permission to change this setting). Once the setting is enabled, go to the Resources page by selecting Resources from the User Account menu and select the Analysis Configuration Templates tab.

Create an Analysis Configuration Template

1. In the Template Name field, enter a unique name of your preference to identify the template.

2. [Optional] In the Template Description field, enter a description for the template.

3. Select the Instrument Platform

   Analysis Configuration Template is currently only supported for NovaSeq X Series and MiSeq i100 Series.

4. Select the analysis location.

   • Cloud - Analyze sequencing data using Illumina pipeline in the cloud.

   • Local - Analyze sequencing data on-instrument.

5. Select an analysis type and version from the Application dropdown.

6. Select the Reference Genome (only applicable if analysis type is not BCL Convert).

7. Enter other settings that are applicable for the selected analysis.

   RNA Differential Expression settings is not supported in Analysis Configuration Template. Please setup the Differential Expression on BaseSpace Sequence Hub after creating the planned run on Clarity.

8. Select Save to save the template.

9. The saved template shall be available on Clarity LIMS. After a run is planned on Clarity LIMS, it can be opened on BaseSpace Sequence Hub Run Planning for further editing. Please note that sample and kit information are not editable.

Edit an existing Analysis Configuration Template

1. To begin editing, click on the template name hyperlink

2. Update the settings

3. Select the Save button to save the changes or the Cancel button otherwise

Delete an existing Analysis Configuration Template

To delete a template, select the trash button located at the right most column.

Use Analysis Configuration Template in Run Planning

You can import settings from an analysis configuration template into a configuration in Run Planning.

1. Click on the "import from Analysis Configuration Template" menu below the Configuration title after selecting an Application version.

2. The Import from Analyis Configuration Template dialog will be displayed.

3. Select the pre-created template to use and click on Confirm button.

   Note that only templates that match the selected Application version will be displayed in the template dropdown.

4. Upon confirmation, the Library prep kit, index adapter kit, barcode mismatches index and analysis settings from the template will be applied to the Configuration.

   Note that existing values in the Configuration (if any) will be overwritten.

5. Complete the Configuration creation with the Samples data and other necessary information.