The documents in this section support the Illumina MiSeq i100 Series integrations with on-premise Clarity LIMS setup.

The integration includes the following:

• Preconfigured MiSeq i100 Series On-Prem Sequencing v2.0 workflow that maps to lab protocols and instrument runs.

• Preconfigured protocols:

  • Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v2.0)

  • Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v2.0)

  • Dilute and Denature (MiSeq i100 Series On-Prem Sequencing v2.0)

  • Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v2.0)

  • AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v2.0)

  • AUTOMATED - Analysis Run (MiSeq i100 Series On-Prem Sequencing v2.0)

• Automatic validation of run setup information before sample sheet generation and planned run creation.

• Automated planned run creation on MiSeq i100 Series instrument via Illumina Run Manager. The planned run created will be retrieved by MiSeq i100 Series Control Software and used to start a sequencing run.

• Automated tracking of the MiSeq i100 Series sequencing run status and parsing of run metrics.

• Automated tracking of the MiSeq i100 Series analysis run status, result summary and demultiplexing result files.

• Support for configuration of secondary analysis with library prep kit (LPK) and index adapter kit (IAK) via Analysis Configuration Template for the planned run. The analysis is performed by DRAGEN on-premise.

• (Optional) Preconfigured Library Prep Validation v2.3.6 workflow used for validation purposes only. The workflow contains a single-step protocol that models the library prep workflow required to produce libraries tagged with index sequences. At the end of the step, these libraries are routed to MiSeq i100 Series On-Prem Sequencing v2.0 workflow.

The integration includes the following:

• Preconfigured MiSeq i100 Series On-Prem Sequencing v1.0 workflow that maps to lab protocols and instrument runs.

• Preconfigured protocols:

Release Date: November 2025

These Release Notes describe the key changes to software components for the Clarity LIMS MiSeq i100 Series On Premise Integration Package version 1.1.0.

Compatibility

Refer to under Instruments & Integrations.

Last Updated: December 2024

Release Date: December 2024

These Release Notes describe the key changes to software components for the Clarity LIMS MiSeq i100 Series On Premise Integration Package version 1.0.0.

Compatibility

Refer to under Instruments & Integrations.

The Illumina MiSeq i100 Series On-Prem Integration Package v1.0.0 supports the integration of Clarity LIMS to MiSeq i100 Series instruments that are on-premise via Illumina Run Manager.

Prerequisites

The Illumina MiSeq i100 Series On-Prem Integration Package v1.1.0 supports the integration of Clarity LIMS to MiSeq i100 Series instruments that are on-premise via Illumina Run Manager.

Prerequisites

The Illumina MiSeq i100 Series On-Prem Integration Package v1.1.0 supports the integration of Clarity LIMS to Illumina MiSeq i100 Series sequencer connected to the Illumina Run Manager platform on premise.

For instructions on validating and troubleshooting the MiSeq i100 Sequencing v2.0 workflow for the integration, refer to MiSeq i100 Series Sequencing v2.0 Workflow User Interaction, Validation and Troubleshooting.

Prerequisites and Assumptions

Analysis Configuration Template

The MiSeq i100 Series Sequencing v2.0 workflow uses analysis configuration templates (ACT) to configure secondary analysis for the planned runs. It is assumed that the required ACTs for your run has been pre-created using Illumina Run Manager UI. Please make sure that the index adapter kit (label group on Clarity) selected in the ACT has already been created on Clarity LIMS. The same label group shall be used in the library preparation step. Names of ACT must be unique. Please refer to the for details on creating ACT on Illumina Run Manager User Interface (UI).

Samples

It is assumed that samples that enter the MiSeq i100 Series Sequencing v2.0 workflow have gone through library preparation and quantification processes before they are assigned to the workflow:

• Samples have been accessioned into Clarity LIMS.

• Sample and library names must contain only alphanumeric, dash, or underscore characters.

• Samples have been run through QC and library prep.

Workflows, Protocols, and Steps

The MiSeq i100 Series On-Premise Integration Package v1.1.0 includes the following workflows:

• Library Prep Validation v2.3.6 (optional, but recommended for validation purposes)

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

Library Prep Validation v2.3.6 Workflow

MiSeq i100 Series Sequencing v2.0 Workflow

Validation Workflow

The Library Prep Validation v2.3.6 workflow allows for validation of the system after installation is complete. This workflow can be replaced by other custom library preparation workflows.

Configure a custom library preparation workflow as follows.

1. Select Configuration, then select Lab Work.

2. Add a Routing Script automation to the last Master Step of the library preparation workflow.
3. Select Configuration, then select Automation.

How the Integration Works

The following information summarizes how the MiSeq i100 Series On-Premise Integration works.

• After the 'Validate Run Setup and Create Planned Run' automation is triggered on the Load to Dry Cartridge step, the run parameters entered in the Run Details screen and the sample informations are sent to Illumina Run Manager. Illumina Run Manager validates the run and analysis configuration before the planned run is created, the automation also generates the sample sheet and attaches it to the step. In the event of incomplete information or misconfiguration on the planned run, an error will be displayed on the automation banner and details of the error will be logged in the automation log file.

• When the sequencing run starts on the instrument, the MiSeq i100 Series Control Software notifies the Illumina Run Manager integration. The events are processed and the integration service retrieves the run information from MiSeq i100 Illumina Run Manager. This information is used to populate the custom fields in the AUTOMATED - Sequencing Run step.

Start a Sequencing Run on MiSeq i100 Series Instrument

To start a planned run, refer to information on .

Enabling Planned Run Generation for Samples Having Duplicate Name with Different Indexes

The library preparation workflow of the samples must be before routing the samples through the library preparation workflow.

Rules and Constraints

• The workflow configuration contains several validation checks. To make sure that the calculations work properly, it is important that you do not disable any of this validation logic. The validation checks determine the following information:

  • Which samples, and how many, can enter each step together.

  • Which samples, and how many, can be pooled together.

This section explains how to validate the installation of the Illumina MiSeq i100 Series On-Prem Integration Package v1.0.0.

The validation process involves the following actions:

• Running samples through the Library Prep Validation v2.3.5 workflow.

  • The workflow contains a single-step protocol that models the library prep required to produce libraries tagged with index sequences. At the end of the step, these libraries are routed to MiSeq i100 Series On-Prem Sequencing v1.0 workflow.

• Running libraries through the MiSeq i100 Series On-Prem Sequencing v1.0 workflow validates the following items:

  • Successful sequential step advancement of samples through the steps of the workflow.

    • Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)

The validation steps assume the following conditions have been met:

• Integration package has been successfully installed. Refer to .

• Analysis configuration templates (ACTs) are created in Illumina Run Manager for your run.

• Index Adapter Kit used in selected ACT is created as label group in Clarity LIMS.

  ℹ For more information on creating a reagent label group, refer to Add and Configure Labels and Label Groups in the

Analysis Configuration Template Creation in Illumina Run Manager

MiSeq i100 Series On-Prem Sequencing v1.0 workflow requires Analysis Configuration Templates (ACTs) for configuring secondary analysis.

Create these ACTs in Illumina Run Manager (IRM) UI:

1. Select Analysis Configuration Templates from the dropdown list of the IRM UI menu icon

2. Select Add analysis template to create and add a new ACT.

3. Fill up details of the ACT and select Save.

For details, refer to the Illumina Run Manager help documentation on Illumina support site.

Activate Workflow, Create Project, Add and Assign Samples

The following steps set up Clarity LIMS in preparation for running samples through the Library Prep Validation v2.3.5 and MiSeq i100 Series On-Prem Sequencing v1.0 workflows.

1. On the Configuration tab, under Workflows, activate both the Library Prep Validation v2.3.5 and MiSeq i100 Series On-Prem Sequencing v1.0 workflows.

2. On the Projects and Samples screen, create a project and add samples to it.

   ⚠ Sample and library names must use only alphanumeric, dash, or underscore characters. Invalid characters can cause a sample sheet validation failure in the Load to Dry Cartridge step.

Library Prep Protocol

This single-step protocol models the library prep required to produce libraries tagged with index sequences that are ready for the MiSeq i100 Series On-Prem Sequencing v1.0 workflow.

Follow the steps in to run the Library Prep Validation workflow with the following:

• Label Group = same as the Index Adapter Kit selected in the ACT that is being used

• Sequencing Instrument = MiSeq i100 Series On-Prem

On exit from the step, the Routing Script automation is triggered. This automation assigns samples to the first step of the MiSeq i100 Series On-Prem Sequencing v1.0 workflow, Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0).

Protocol: MiSeq i100 Series On-Prem Sequencing v1.0

The MiSeq i100 Series On-Prem Sequencing v1.0 protocol consists of the following steps:

• Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)

• Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0)

• Load To Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0)

Step 1: Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)

1. In Lab View, locate the MiSeq i100 Series On-Prem Sequencing v1.0 protocol. The samples are queued for the Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0) step.

2. Add the samples to the Ice Bucket and start the step. The Validate Sample Names automation is triggered upon step started, and validates the sample names.

3. Select the connected MiSeq i100 instrument to integrate with.

Step 2: Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0)

1. In Lab View, locate the MiSeq i100 Series On-Prem Sequencing v1.0 protocol. The samples are queued for the Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0) step.

2. Add the samples to the Ice Bucket and select View Ice Bucket.

3. On the Ice Bucket screen, select Begin Work.

1. On the Record Details screen, navigate to the Reagent Lot Tracking section to track the lot information used in the step.

   [Optional] Create a new lot. For more information, refer to Add and Configure Reagent Kits and Lots in the .

2. In the Step Details area, complete the following fields:

Step 4: Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0)

1. In Lab View, locate the MiSeq i100 Series On-Prem Sequencing v1.0 protocol. The pool of samples are queued for the Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0) step.

2. Add the pool to the Ice Bucket and select View Ice Bucket.

   ⚠ Only single pool is allowed at this step.

Step 5: AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0)

User interaction is not required, but you can review the stages of the step in Clarity LIMS.

Review Run Data

Read summary metrics are recorded for the library pool. After the run is complete, open the step and review these metrics in the Step Details section and the Sample Details table.

Step 6: AUTOMATED - Analysis Run (MiSeq i100 Series On-Prem Sequencing v1.0)

User interaction is not required, but you can review the stages of the step in Clarity LIMS. If the run analysis tracking is successful, the integration completes the step automatically.

Review Analysis Data

After the analysis run is complete, open the step and review the following values in the Step Details section:

• Analysis Status - Status of the analysis run

• Analysis Result Location - Location of the secondary analysis data. This field is empty if transfer of secondary analysis data to an external location is disabled.

• Log - Log message when integration handling the event from IRM

File placeholder:

• Demultiplexing results file - demultiplexing statistics for each sample

At this point, the entire MiSeq i100 Series On-Prem Integration workflow is fully validated.

Troubleshooting

If an automation trigger does not appear to run its corresponding scripts, refer to the Troubleshooting Automation section in the .

Validate Analysis Configuration Automation Check Fails

The Validate Analysis Configuration automation check is in the Make Bulk Pool (upon pooling) step. If a failure happens, an error message displays and the step can be aborted, or you might be prevented from continuing the step.

This check can fail for the following reasons:

• Pooled samples assigned with the same secondary analysis application must have the same analysis version (e.g. v3.8.4) and settings (e.g. Map/Align Output Format = CRAM).

  Resolve this error as follows.

Error When Creating Planned Runs

If you receive an error when creating a planned run, check the log message in the Load to Dry Cartridge step to identify the issue. If you cannot correct the issue, contact Illumina Support.

Incompatible Analyses in a Planned Run

Only compatible analysis versions should be combined in a single planned run. When incompatible analysis versions are combined, an error log message displays. An example of the error log message is shown below.

To resolve this error, check the ACTs that were used for the run. Create a new planned run with ACTs that have the same analysis and analysis versions.

Automated Step Does Not Start

If the AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0) step does not start, Clarity LIMS is likely not receiving sequencing run events from Illumina Run Manager correctly. Check for the following issues:

• The instrument must be reflected as Connected and Active in the Illumina Run Manager Integration UI. Reconnect the instrument if the status reflects otherwise.

• The container must be queued at the AUTOMATED - Sequencing Run step. It should not be in the ice bucket or in the previous step.

If the issues remain, contact Illumina Support.

Automated Step Starts, But Does Not Complete

If the AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0) step starts, but does not complete, do as follows.

1. Log in to the default user account and search for the in progress step in Clarity LIMS using the container name as the search term.

2. On the Record Details screen, the Sequencing Log multiline text field contains logging information.

   If unable to reach the Record Details screen, or if the Sequencing Log field does not contain enough information to resolve the issue, contact Illumina Support. Provide the relevant information from the troubleshooting steps already performed.

The Illumina MiSeq i100 Series On-Prem Integration Package v1.0.0 supports the integration of Clarity LIMS to Illumina MiSeq i100 Series sequencer connected to the Illumina Run Manager platform on premise.

For instructions on validating and troubleshooting the Illumina MiSeq i100 Series On-Premise Integration, refer to MiSeq i100 Series On-Premise Integration v1.0.0 User Interaction, Validation and Troubleshooting.

Prerequisites and Assumptions

Analysis Configuration Template

The MiSeq i100 Series On-Prem Sequencing v1.0 workflow uses analysis configuration templates (ACT) to configure secondary analysis for the planned runs. It is assumed that the required ACTs for your run has been pre-created using Illumina Run Manager UI. Please make sure that the index adapter kit (label group on Clarity) selected in the ACT has already been created on Clarity LIMS. The same label group shall be used in the library preparation step. Names of ACT must be unique. Please refer to the for details on creating ACT on Illumina Run Manager User Interface (UI).

Samples

It is assumed that samples that enter the MiSeq i100 Series On-Prem Sequencing v1.0 workflow have gone through library preparation and quantification processes before they are assigned to the workflow:

• Samples have been accessioned into Clarity LIMS.

• Sample and library names must contain only alphanumeric, dash, or underscore characters.

• Samples have been run through QC and library prep.

Workflows, Protocols, and Steps

The MiSeq i100 Series On-Premise Integration Package v1.0.0 includes the following workflows:

• MiSeq i100 Series On-Prem Sequencing v1.0

• Library Prep Validation v2.3.5 (optional, but recommended for validation purposes)

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

Library Prep Validation v2.3.5 Workflow

MiSeq i100 Series On-Prem Sequencing v1.0 Workflow

Validation Workflow

The Library Prep Validation v2.3.5 workflow allows for validation of the system after installation is complete. This workflow can be replaced by other custom library preparation workflows. For details, refer to .

[Optional] Configure a custom library preparation workflow. Routing of libraries from the custom workflow to the MiSeq i100 Series On-Premise Sequencing protocol can be enabled in the master step with the available in the NGS package.

Step 1: Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)

In this step, secondary analyses are configured for the samples using ACTs. Each ACT contains details related to a particular secondary analysis (e.g., index adapter kit to use, reference genome setting). At this step, the user selects an ACT from a list of pre-constructed ACTs and assigns samples to it. A planned run can involve multiple ACTs and users have to repeat Step 1 for each ACT that is required for the planned run. For more information on creating ACTs and assigning samples to them, refer to .

Master Step Fields

The following table lists the configuration details for custom fields that are defined on the Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0) step.

Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0) Master Step Field Configuration

Global Fields

The following lists the global custom fields that are configured to display on the Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0) step. See Global Fields section for detail configuration.

• Molarity (nM)

• ACT Name

Step 2: Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0)

Samples are pooled in the Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0) step. You can manually create working pools based on the final loading concentration required.

Master Step Fields

The following table lists configuration details for the custom fields that are defined on the Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0) step.

Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0) Master Step Field Configuration

Global Fields

The following lists the global custom fields that are configured to display on the Make Bulk Pool (MiSeq i100 Series On-Prem Sequencing v1.0) step. See Global Fields section for detail configuration.

• Final Loading Concentration (pM)

• RSB Volume (ul)

• MiSeq i100 Series Flowcell Type

Step 4: Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0)

In this step, the user scans the dry cartridge barcode into the LIMS, and then manually places the working pools into the dry cartridge to be used in the MiSeq i100 Series run. In addition, this step validates the run setup and analysis information and generates samplesheet file and/or creates a planned run on instrument's Illumina Run Manager UI.

Master Step Fields

The following table shows the master step fields that are configured on the Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0) step. These fields are required for sample sheet generation and planned run creation in Illumina Run Manager.

Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0) Master Step Field Configuration

Step 5: AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0)

In this step, the pooled samples in the dry cartridge are sequenced on the MiSeq i100 Series instrument.

There are no automation associated to this step.

Master Step Fields

The following tables show the master step fields that are configured on the AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0) step.

Master Step Field Information

All the fields above are Read-Only Text field, except Sequencing Log is a Read-Only Multiline Text.

Global Fields

The following global custom fields are used to capture the run metrics in Clarity LIMS:

• % Aligned R1

• % Aligned R2

• % Bases >=Q30 R1

• % Bases >=Q30 R2

At the end of the step, the pools of samples are automatically route to next step.

Step 6: AUTOMATED - Analysis Run (MiSeq i100 Series On-Prem Sequencing v1.0)

Data from the analysis is parsed back to Clarity LIMS. In this step, the secondary analysis configured using the Analysis Configuration Template (ACT) is performed on DRAGEN on-premise.

There are no automation associated to this step.

Master Step Fields

The following tables show the master step fields that are configured on the AUTOMATED - Analysis Run (MiSeq i100 Series On-Prem Sequencing v1.0) step.

AUTOMATED - Analysis Run (MiSeq i100 Series On-Prem Sequencing v1.0) Master Step Field Information

All the fields above are Read-Only Text field, except Log is a Read-Only Multiline Text.

How the Integration Works

The following information summarizes how the MiSeq i100 Series On-Premise Integration works.

• After the 'Validate Run Setup and Create Planned Run' automation is triggered on the Load to Dry Cartridge (MiSeq i100 Series On-Prem Sequencing v1.0) step, the run parameters entered in the Run Details screen and the sample informations are sent to Illumina Run Manager. Illumina Run Manager validates the run and analysis configuration before the planned run is created, the automation also generates the sample sheet and attaches it to the step. In the event of incomplete information or misconfiguration on the planned run, an error will be displayed on the automation banner and details of the error will be logged in the automation log file.

• When the sequencing run starts on the instrument, the MiSeq i100 Series Control Software notifies the Illumina Run Manager integration. The events are processed and the integration service retrieves the run information from MiSeq i100 Illumina Run Manager. This information is used to populate the custom fields in the AUTOMATED - Sequencing Run (MiSeq i100 Series On-Prem Sequencing v1.0) step.

Start a Sequencing Run on MiSeq i100 Series Instrument

To start a planned run, refer to information on .

Enabling Planned Run Generation for Samples Having Duplicate Name with Different Indexes

The library preparation workflow of the samples must be before routing the samples through the library preparation workflow.

Components Installed

The following sections describe the components (files, properties, reagent categories / label groups, reagent kits, and containers) that are installed by default as part of this integration.

Global Fields

Container Global Fields

Derived Sample Global Fields

Reagent Kits

• MiSeq i100 Series Dry Cartridge

• MiSeq i100 Series Library Denature (KLD)

• MiSeq i100 Series Wet Cartridge

Container Types

• MiSeq i100 Series Dry Cartridge

Instrument Types

• MiSeq i100 Series

Rules and Constraints

• The workflow configuration contains several validation checks. To make sure that the calculations work properly, it is important that you do not disable any of this validation logic. The validation checks determine the following information:

  • Which samples, and how many, can enter each step together.

  • Which samples, and how many, can be pooled together.