Upgrading to MiSeq Control Software v4.0

What is the upgrade?
The MiSeq system upgrade is accomplished by updating to MiSeq Control Software (MCS) v4.0. MCS v4.0 provides several updates:
  • Upgrade to Windows 10 operating system and installation of a new hard drive
  • Update MiSeq System Suite to v4.0
  • Update to Local Run Manager (LRM) v3, which replaces LRM v2 or MiSeq Reporter. This provides the following enhancements:
    • Simplified run setup and onboard analysis
    • New password recovery feature using security questions for unlocking user accounts
    • Improved account security features
    • Improved handling of decoupled Library Prep Kits and Index Kits
  • The upgrade must be performed by an Illumina Field Service Engineer or Field Applications Scientist
Software changes for the MiSeq System Suite v4.0 are found in the MiSeq v4.0 Software Release Notes. Up-to-date Windows 10 upgrade information for all Illumina Sequencing Systems is found on the Windows 10 Upgrade Support page.
Upgrade Process
  • To upgrade the MiSeq to Windows 10 and MiSeq System Suite v4.0, contact Illumina Technical Support with the instrument serial number.
  • To ensure a smooth upgrade, the Illumina field support team will contact you to complete a pre-upgrade check list and the Network Set-up Questionnaire.
  • Coordinate and schedule the upgrade with your Illumina field team after they receive the required information.
  • If the MiSeq instrument is covered by an active service contract or first year warranty, the upgrade is provided at no additional cost.
  • Upgrades are available for instruments not on a service contract as a billable service.
  • After the upgrade, the control software cannot be downgraded to the previous version.
  • Limited LRM modules are available at first release and Clarity LIMS Integration is not yet supported. Discuss an upgrade strategy with your Illumina field team that best fits your needs during the pre-upgrade check list evaluation.
New interface of MCS v4.0
MCS v4.0 has an updated home screen, which includes Sequence and Wash options to start runs and perform instrument washes. Additional functions including instrument shutdown, system settings, system check, and file management are available through the hamburger menu located in the left upper corner of the screen.
Run Setup with MiSeq Control Software v4.0
Options for run set up include LRM mode, Sample Sheet mode, or Manual mode. All options allow for uploading runs to BaseSpace Sequence Hub (BSSH) for Run Monitoring. Additionally, LRM mode allows for upload to BSSH for run analysis, collaboration, and storage. BaseSpace Onsite has been discontinued and is not compatible with MCS v4.0.
The MiSeq System Guide includes instructions for run setup. LRM run set up is simple and the preferred option for run setup. If LRM is new to you, we strongly recommend completing the 20 minute interactive Local Run Manager v3 course. Illumina also hosts a LRM v3 introduction webinar.
Sample sheets in MCS v4.0
  • Sample sheets created in Illumina Experiment Manager (IEM) are not compatible with MCS v4.0. IEM sample sheets CANNOT be imported in MCS v4.0 Run Setup Option Sample Sheet mode. Only LRM sample sheets are compatible.
  • To create a sample sheet, download the sample sheet template from the desired LRM module page, populate it manually, and upload it into the LRM module.
  • Template sample sheets are posted and more information about sample sheet fields are included in the MiSeq Sample Sheet Quick Reference Guide.
Important information about LRM v3.0
  • At launch, available LRM v3.0 modules are Generate FASTQ 3.0, Library QC 2.1, and Resequencing 3.0.
  • DNA Enrichment 3.0, DNA Amplicon 3.0, and other modules will be available shortly after launch.
  • If necessary LRM analysis modules are not available yet, use alternative analysis apps available on BSSH.
  • For some workflows, scheduling the upgrade when more LRM modules are available may be the preferred option.
  • LRM v1, v2, v3, and Dx modules are unique to each framework and cannot be cross-installed.
  • To check for newly released modules, use the LRM module selector.
Networking considerations
Setting the output folder to a network location has special considerations due to Windows 10 authentication requirements. Windows 10 requires users to update passwords periodically. To configure the network, work with your IT team and follow the instructions in How to connect benchtop instruments and Local Run Manager to a network location.
For any feedback or questions regarding this article (Illumina Knowledge Article #5753), contact Illumina Technical Support [email protected].
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