MiSeq Integration v8.0 Configuration and User Interaction

The Illumina MiSeq Integration Package v8.0 includes the following features:

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Preconfigured MiSeq Sequencing v3.0 workflow that maps to lab protocol steps and sequencing runs.

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Automated generation of a sample sheet for use with the MiSeq Control Software (MCS) and Local Run Manager.

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Supported Local Run Manager analysis modules are GenerateFastQ, Library QC, Resequencing, DNA Enrichment, and DNA Amplicon.

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Automated tracking of the MiSeq sequencing run and parsing of run statistics into Clarity LIMS, including:

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Run status and metrics of sequencing run

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Sequencing run parameters

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Real-Time Analysis (RTA) v1 run directory location and other run-specific information

This integration also includes a preconfigured Library Prep Validation workflow that is used for validation purposes only. The workflow contains a single-step protocol that models the library prep required to produce normalized libraries that are ready for the MiSeq Sequencing v3.0 workflow. For details, see MiSeq Integration v8.0 Validation and Troubleshooting.

Depending on the Clarity LIMS version, install the workflows as follows.

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For Clarity LIMS v4 (4.2 and later), install the following workflows via Preconfigured Workflows Package (PCWP) v2.1:

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MiSeq Sequencing v3.0 workflow

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Library Prep Validation v1.1.2 workflow

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For Clarity LIMS v5 (5.1 and later), install the following workflows via Illumina Preset Protocols (IPP) v2.1:

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MiSeq Sequencing v3.0 workflow

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Library Prep Validation v2.0.2 workflow

The following sections describe the MiSeq Sequencing v3.0 workflow.

For instructions on validating and troubleshooting the Illumina MiSeq Integration Package, see MiSeq Integration v8.0 Validation and Troubleshooting.

MiSeq Integration v8.0 is not supported on Clarity LIMS v5.0.

MiSeq Integration v8.0 is only required for MCS (MiSeq Control Software) v4.0. For users on MCS v3.1 and earlier, refrain from upgrading to MiSeq Integration v8.0 as it breaks the integration.

MiSeq Sequencing v3.0 workflow is only compatible with MiSeq INT v8.0 package.

Before samples are assigned to the workflow, make sure that the following prerequisites are completed.

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Samples have been run through QC and library prep.

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Samples have been normalized, and the value is captured in a field called Normalized Molarity (nM).

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Reagent labels are attached to samples.

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Samples have been accessioned into Clarity LIMS.

For more information on sample accessioning, see Sample Accessioning and Upload and Modify Samples in the Clarity LIMS Core Functionality documentation.

Samples can be assigned to the MiSeq Sequencing v3.0 workflow automatically using a routing script or manually from the Projects & Samples dashboard. See Assign and Process Samples in the Clarity LIMS Core Functionality documentation.

The Illumina MiSeq Integration includes the MiSeq Sequencing v3.0 workflow, which contains a single protocol of the same name.

The protocol includes the following steps and automations.

MiSeq Sequencing v3.0 Protocol Steps and Automations

Step	Automation
1. Library Pooling (MiSeq v3.0)	• Validate Maximum Number of Samples • Set Next Step - Advance
2. Denature and Dilute (MiSeq v3.0)	• Validate Run Setup and Generate MiSeq SampleSheet • Set Next Step - Advance
3. MiSeq Run (MiSeq v3.0)	• Set Next Step - Advance

This integration supports Clarity LIMS v4.2 and later.

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:

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Master step fields—Configured on master steps. Master step fields only apply to the following:

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The master step on which the fields are configured.

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The steps derived from those master steps.

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Global fields—Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.