Last updated
Last updated
The Illumina NovaSeq 6000 Integration v2.6.0 supports the integration between Clarity LIMS and the NovaSeq 6000 instrument. This integration also provides support for Clarity LIMS v6.2.0 and includes updates to the technology stack and third party libraries and utilities.
Clarity LIMS is automatically stopped during installation of the RPM and will need to be restarted. The file-based and API-based integrations cannot run at the same time. When the API-based integration has finished installing, shut down Clarity LIMS and uninstall the file-based integration.
This document provides instructions for installing NovaSeq 6000 Integration v2.6.0. It also describes the components that are installed in the default configuration.
For details on installed protocols and steps, automations, generated and captured files, and rules and constraints, refer to .
For information on user interaction for each step, validating and troubleshooting the integration, refer to .
NovaSeq 6000 Integration v2.6.0 has the following prerequisites:
Mount run data network-attached storage (NAS) share
Secret Util is installed
IPP is installed
NovaSeq 6000 Integration v2.6.0 supports both on-premise and cloud integrations. This integration is distributed as the following RPM packages:
BaseSpaceLIMS-novaseq-extensions
BaseSpaceLIMS-novaseq-sequencing-service (depends on BaseSpaceLIMS Automation Worker v1.x)
The BaseSpaceLIMS-novaseq-extensions RPM installs the following items:
Protocols and steps
Validation workflow
Integration properties that configure the service
novaseq-extensions.jar file that provides sample sheet generation and other utility scripts
The BaseSpaceLIMS-novaseq-sequencing-service RPM installs the following items:
Bash scripts to run the novaseq_seqservice through systemctl
novaseq-sequencing.jar
novaseq-remote-extensions.jar file that contains scripts that need access to the run folders on the NAS
Use the following instructions to install the BaseSpaceLIMS-novaseq-extensions and BaseSpaceLIMS-novaseq-sequencing-service RPMs on the Clarity LIMS server.
The BaseSpaceLIMS-novaseq-extensions RPM must be installed on the Clarity LIMS server. The BaseSpaceLIMS-novaseq-sequencing-service RPM can be installed remotely on another server within the network.
The configuration provided with this integration has been established to support NovaSeq 6000 lab processes. Any configuration changes to protocols or workflows, including renaming protocols, steps, and fields, could break processes.
The NovaSeq instrument software includes the following components:
NovaSeq Control Software (NVCS) — Contains the user interface for setting up the sequencing run. Responsible for controlling the instrument and acquiring the images.
Real-Time Analysis v3 (RTA3) — Takes the images generated by the first module, processes, and analyzes them. Makes sure that data files are created and copied to the final destination folder.
Sequencing Analysis Viewer (SAV) — Displays the important quality metrics generated by the RTA3 software.
NovaSeq recipes — Provides system operation instructions for use with NovaSeq 6000 reagent kits for SP, S1, S2, and S4 flow cells.
Universal Copy Service — Copies output files to destinations such as final destination folder and/or BaseSpace Sequence Hub (when the instrument is configured for use with BaseSpace Sequence Hub).
For the NovaSeq API integration to work, the NovaSeq instrument must be able to communicate with Clarity LIMS through the API. Complete the following steps to configure the NVCS and confirm that you can access Clarity LIMS from the instrument.
Launch NVCS and wait for the initialization process to complete.
On the NVCS Settings page, do the following:
Under Mode Selection, select File-Based.
In the adjacent field, enter the network folder location that NVCS retrieves the JSON recipe from.
In the Output Folder field, enter the default output folder location.
Select Save to complete the configuration.
On the NVCS home page, you can now select Sequence to log into Clarity LIMS and start a run.
For more information on installing Secret Util with the Integration Module, refer to Install/Upgrade Secret Management for Integration Modules in the .
For a custom API username, set the to apiusers/{custom API username} (e.g., apiusers/novaseq_user). For more information on Secret Utility configuration, refer to the .
For more information on the configurable integration properties that enable capture and generation of files associated with the sequencing run, refer to .
The sample sheet, run recipe, and run output folders can all be configured independently and do not have to be on the same mount or share. For examples of valid configuration mount points and properties, refer to .
Oracle Linux (for compatibility, refer to )
Minimum requirements for remote Automation Worker (for more information, refer to the )
ℹ If you are running the sequencing service and Automation Worker on the same instance, make sure that the instance is running a compatible version of Oracle Linux. For compatibility, refer to .
For more information on installing Secret Util with the Integration Module, refer to Install/Upgrade Secret Management for Integration Modules in the .
For a custom API username, set the to apiusers/{custom API username} (e.g., apiusers/novaseq_user). For more information on Secret Utility configuration, refer to the .
For more information on the configurable integration properties that enable capture and generation of files associated with the sequencing run, refer to .
The sample sheet, run recipe, and run output folders can all be configured independently and do not have to be on the same mount or share. For examples of valid configuration mount points and properties, refer to .
For more information on the configurable integration properties that enable capture and generation of files associated with the sequencing run, refer to
The sample sheet, run recipe, and run output folders can all be configured independently and do not have to be on the same mount or share. For examples of valid configuration mount points and properties, refer to .
For detailed descriptions of the steps and automations included in each protocol, and details on other components in the configuration, refer to .
For instructions on using the NovaSeq Validation Library Prep (NovaSeq 6000 v2.3) protocol, refer to .