Frequently asked questions about upgrading to MiSeq Control Software v4.0

MiSeq Control Software v4.0 (MCS) New Features Include:
  • Windows 10 compatibility: Initially, MiSeq instruments operated with Windows 7, which was obsolesced by Microsoft at the end of 2019.
  • Improved Real-Time Analysis (RTA) version for improved base calling accuracy.
  • Enhanced Illumina Proactive monitoring capabilities for increased instrument uptime.
  • Integration of Local Run Manager v3 (LRM).
  • LRM replaces MiSeq Reporter (MSR).
  • New interface for starting run, performing washing and additional functions.
  • Improved file copy process with Universal Copy Service (UCS) v1.6.3, which copies files to a local location, network, and BaseSpace.
Frequently Asked Questions:
Are the installers for MCS v4.0 available to download online?
  • No. The update must be performed by an Illumina engineer or field application scientist as the update requires installation of new hard drives. Contact [email protected] for questions and to schedule the update.
What are the benefits of LRM and onboard analysis?
  • LRM streamlines run set-up and downstream data analysis. Customers can choose from various analysis modules or automate FASTQ generation for incorporation into analysis pipelines. Because the process is computationally intensive, no additional operations should be performed on the instrument during onboard analysis, including sequencing.
What are the available LRM modules at launch?
  • Generate FASTQ 3.0
  • Library QC 2.1
  • Resequencing 3.0
Can I use sample sheets created in Illumina Experiment Manager for run setup?
  • No. Sample sheets created in Illumina Experiment Manager are not compatible with MCS v4.0. Template sample sheets can be downloaded for the desired LRM module, populated manually, and uploaded into the LRM module.
Is the instrument connected to Illumina Proactive after the upgrade?
  • Illumina Proactive settings are retained after the upgrade. To change the settings, inform your field service engineer upon install.
What training is available for my group to learn LRM?
Does this upgrade include Windows 10?
  • Yes. New hard drives are installed with Windows 10 OS as part of the upgrade.
How do I schedule my upgrade?
  • Contact [email protected] to request the MCS v4.0 and Windows 10 upgrade on installed MiSeq instruments.
For any feedback or questions regarding this article (Illumina Knowledge Article #5752), contact Illumina Technical Support [email protected].
Last modified 23d ago
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