NovaSeq X Series Integration v1.0 Configuration and User Interaction

The Illumina NovaSeq X Series Integration Package v1.0 supports the integration of Clarity LIMS to Illumina NovaSeq X series instruments. This integration supports Clarity LIMS v5.1 and later.

For instructions on validating and troubleshooting the Illumina NovaSeq X Series Integration, refer to NovaSeq X Series Integration v1.0 Validation and Troubleshooting.

The configuration provided in this integration has been established to support NovaSeq X Series lab processes. Any configuration changes to protocols or workflows (including renaming protocols, steps, and fields) could break the process.

The integration includes the following features:

• Preconfigured NovaSeq X Series Sequencing v1.0 workflow that maps to lab protocols and instrument runs.
• The following steps in the NovaSeq X Series Sequencing v1.0 preconfigured protocol:
– Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.0)
– Make Bulk Pool (NovaSeq X Series Sequencing v1.0)
– Dilute and Denature (NovaSeq X Series Sequencing v1.0)
– Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0)
– AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.0)
• Automatic validation of run setup information before sample sheet generation or planned run creation.
• Automated generation of the sample sheet. This sample sheet is used to start the sequencing run on the NovaSeq X Series Control Software through Local run mode.
• Automated creation of a planned run on Illumina Connected Analytics (ICA). The NovaSeq X Series Control Software retrieves the planned run for use with the Cloud run mode.
• Automated tracking of the NovaSeq X Series sequencing run and parsing of run statistics into Clarity LIMS using the Stratus Integration Service (SIS).
• [Optional] Preconfigured Library Prep Validation v2.3.0 workflow used for validation purposes only. The workflow contains a single-step protocol that models the library prep required to produce libraries that are ready for the NovaSeq X Series Sequencing v1.0 workflow. For more information, refer to NovaSeq X Series Integration v1.0 Validation and Troubleshooting. The Library Prep Validation v2.3.0 workflow is available in the Illumina Preset Protocols (IPP) v2.5 package.
• [Optional] Clarity LIMS Product Analytics integration that can be used with ICA. The Clarity LIMS Product Analytics integration installation and configuration is required. For more information, refer to Clarity LIMS Product Analytics Service Integration v1.1 Installation and Clarity LIMS Product Analytics Integration v1.1 Configuration and User Interaction.

The NovaSeq X Series Sequencing v1.0 workflow uses analysis configuration templates (ACTs) to configure secondary analysis for planned runs. Required ACTs must be created using BaseSpace Sequence Hub. The index adapter kit (the label group in Clarity LIMS) selected in the ACT is created in Clarity LIMS. The same label group must be used in the library preparation step. For more information, refer to NovaSeq X Series Integration v1.0 Validation and Troubleshooting.

Make sure that ACT names created in BaseSpace Sequence Hub do not have leading or trailing spaces. Otherwise, Clarity LIMS can have issues with recognizing the ACT names.

Samples must go through the library preparation and quantification process before they enter the NovaSeq X Series Sequencing v1.0 workflow. It is assumed that the following steps have completed before samples are assigned to the workflow:

• Samples have been accessioned into Clarity LIMS.
• Samples have been run through QC and library prep.
• Samples have the Molarity (nM) global field set to a value. This value is required for the Calculate Volumes automation in the Make Bulk Pool step.

For more information on sample accessioning, refer to Sample Accessioning and Upload and Modify Samples in the Getting Started section of the Clarity LIMS Core Functionality documentation.

You can assign samples to workflows automatically, using a routing script, or manually—from the Projects & Samples dashboard. Refer to Assign and Process Samples in the Clarity LIMS Core Functionality documentation.

The NovaSeq X Series Integration Package v1.0 includes the following workflows:

• NovaSeq X Series Sequencing v1.0
• Library Prep Validation v2.3.0 (optional, but recommended for validation purposes)

The following table describes the protocols and steps included in these workflows.

NovaSeq X Series Integration Package v1.0 Protocols and Steps

Protocol Name

Protocol Purpose

Protocol Steps

Library Prep Validation v2.3.0 Workflow

Library Prep Validation v2.3.0

Included for validation purposes only, this protocol models the library prep steps required to advance samples to the NovaSeq X Series Sequencing v1.0 workflow.

The protocol contains a single step - Library Prep Validation v2.3.0. After this step, a routing script sends the samples to the first step of the NovaSeq X Series Sequencing v1.0 workflow (Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.0)).
1. Library Prep Validation v2.3.0

NovaSeq X Series Sequencing v1.0 Workflow

NovaSeq X Series Sequencing v1.0

Allows for the assignment of per sample values for the following properties:

1. Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.0)
• The secondary analysis of samples is configured using the ACT.
• The labels applied to the samples are validated against the selected ACT so that samples use valid labels.
2. Make Bulk Pool (NovaSeq X Series Sequencing v1.0)
• The Calculate Volumes script assists with pooling samples and adding resuspension buffers and reagents.
• The Validate Analysis Configurations automation validates the ACT of pooled samples to make sure that the secondary analysis configurations remain valid after pooling.
3. Dilute and Denature (NovaSeq X Series Sequencing v1.0)
• The Calculate Volumes script helps denature and dilute samples from step 2 to the final loading concentration.
4. Load To Library Tube Strip (NovaSeq X Series Sequencing v1.0)
• The library pools from step 3 are ready to be loaded to the NovaSeq X Series library tube strip.
• Validates run and analysis information.
• Generates the sample sheet and creates the planned run.
5. AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.0)
• The step is fully automated and starts and completes automatically after the sequencing run is started and completed on the instrument side.
• The sequencing run metadata (eg, run configuration, primary run metrics, and so on) are recorded automatically.
• The integration does this step automatically. Do not add samples to the Ice Bucket or start or complete the step.
1. Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.0)
2. Make Bulk Pool (NovaSeq X Series Sequencing v1.0)
3. Dilute and Denature (NovaSeq X Series Sequencing v1.0)
4. Load To Library Tube Strip (NovaSeq X Series Sequencing v1.0)
5. AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.0)

The Library Prep Validation v2.3.0 workflow allows for validation of the system after installation is complete. For details, refer to NovaSeq X Series Integration v1.0 Validation and Troubleshooting.

The following table lists the step automations included in the NovaSeq X Series Sequencing v1.0 workflow. Automation details are provided in the documentation for each step.

For details on the validation workflow, refer to NovaSeq X Series Integration v1.0 Validation and Troubleshooting.

NovaSeq X Series Sequencing v1.0 Workflow Step Automations

Protocol

Step

Automation

NovaSeq X Series Sequencing v1.0
1. Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.0)

Register Step Completed¹

Retrieve ACT Information

Validate Reagent Labels and Apply Selected ACT to Samples and Set Next Step

Validate Sample Names and Retrieve Analysis Configuration Template List and Register Step Started²
2. Make Bulk Pool (NovaSeq X Series Sequencing v1.0)

Calculate Volumes

Register Pools and Register Step Completed¹

Register Step Started¹

Set Next Step

Validate Analysis Configurations
3. Dilute and Denature (NovaSeq X Series Sequencing v1.0)

Calculate Volumes

Register Step Completed¹

Set Next Step

Validate Inputs Flowcell Type and Register Step Started²
4. Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0)

Register Step Completed¹

Set Next Step

Validate Analysis Configurations and Register Step Started²

Validate Library Tube Strip Barcode

Validate Run Setup and Create Planned Run
5. AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.0)

Register NovaSeq X RunCompleted and Register Step Completed¹

Register Step Started and Register NovaSeq X Run and Register NovaSeq X Run Association and Register NovaSeq X RunStarted¹

¹ These automations are required for Clarity LIMS Product Analytics support only.

² These automations are required for the NovaSeq X Series Sequencing v1.0 workflows and contain additional logic needed for Clarity LIMS Product Analytics support. If you would like to remove support for Clarity LIMS Product Analytics, contact Illumina Support.

All remaining automations are required for the NovaSeq X Series Sequencing v1.0 workflows.

The Illumina Universal Sample Identifier is a global field that is imported with the Library Prep Validation v2.3.0 and NovaSeq X Series Sequencing v1.0 workflows. Illumina Universal Sample Identifier is a text field that is reserved for Clarity LIMS Product Analytics support. The field is optional and not required for this integration.

As of Clarity LIMS v5, the term user-defined field (UDF) has been replaced with custom field in the user interface. However, the API resource is still called UDF.

There are two types of custom fields:

• Master step fields—Configured on master steps. Master step fields only apply to the following:
• The master step on which the fields are configured.
• The steps derived from those master steps.
• Global fields—Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.