Configuration
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.
The configuration provided in this integration has been established to support MiSeq i100 Series lab processes. Any configuration changes to protocols or workflows (including renaming protocols, steps, and fields) could break the integration.
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 MiSeq i100 Sequencing 2.0 Workflow User Interaction, Validation and Troubleshooting for details on creating ACT on Illumina Run Manager User Interface (UI).
Clarity LIMS trims all leading and trailing spaces from the ACT names and ACTs created in Illumina Run Manager UI with names containing leading and/or trailing spaces may not be recognized properly on Clarity. Please ensure that the ACT do not have leading and/or trailing spaces.
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.
Samples have the Molarity (nM) global field set to a valid value (required for the 'Calculate Volumes' automation in the Make Bulk Pool step).
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.
Select Configuration, then select Lab Work.
Add a Routing Script automation to the last Master Step of the library preparation workflow.
Select Configuration, then select Automation.
Create a new Routing Script automation and update it as follows.
For Channel Name, enter limsserver.
For Command Line, enter the following script:
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'MiSeq i100 Series' \ --WORKFLOW 'MiSeq i100 Series Sequencing v2.0' \ --STEP 'Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v2.0)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'"For Automation Use, select the custom library preparation workflow.
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.
Other run events follow the same information flow. When sequencing is complete, the control software uploads the sequencing run data (primary metrics). Then, Illumina Run Manager integration retrieves the primary metrics and uses them to populate the fields in the Sample Details table (e.g., % Error Rate R1). The custom fields (e.g., Run Status, Current Read, and so on) on the AUTOMATED - Sequencing Run step are updated using the run related information. If the sequencing run is successfully completed, the step automatically completes.
The integration tracks the analysis events and results in the AUTOMATED - Analysis Run step. The secondary analysis results are in the external storage configured in Illumina Run Manager. The external storage information is found in the External Storage for Analysis Results configuration settings in Illumina Run Manager.
If a planned run with the same sample name and project name (case-insensitive) has been created previously in Illumina Run Manager, the sample sheet generated from the 'Validate Run Setup and Create Planned Run' automation can reflect the original case of the previous sample name. This can cause validation errors for analysis configurations with sample-level settings. To resolve this issue, change the sample name or the project name on Clarity LIMS and run the automation again.
Start a Sequencing Run on MiSeq i100 Series Instrument
To start a planned run, refer to information on starting a planned run in the Illumina support site..
Enabling Planned Run Generation for Samples Having Duplicate Name with Different Indexes
The library preparation workflow of the samples must be configured to ensure unique derived sample names 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.
For all submitted samples that require analysis, they must have an associated secondary analysis that is configured using the analysis configuration template (ACT). The ACT must be configured on MiSeq i100 Illumina Run Manager before starting the Assign Analysis Configuration Template step. The ACT names must be unique.
Assign Analysis Configuration Template step does not support pool library as input.
The dry cartridge barcode must be unique. There must not be multiple dry cartridge containers with the same name in the Clarity LIMS system.
Reagent labels, or indexes, must be unique.
One library pool can only contain one library or control with no label/index.
The AUTOMATED - Sequencing Run and AUTOMATED - Analysis Run steps must not be manually started or completed. These steps are fully automated and the integration service does not update samples correctly if they have been manually started.
For the automated run to start successfully, you must click 'Validate Run Setup and Create Planned Run' in the Load to Dry Cartridge step and the automation must be ran successfully.
Last updated
Was this helpful?