MiSeq Software Suite v4 Upgrade

The MiSeq Software Suite v4 provides several enhancements to the MiSeq RUO system, including:

  • Windows 10 operating system (OS) upgrade from Windows 7
  • Includes MiSeq Control Software (MCS) v4
  • Introduction of Local Run Manager v3 for simplified run setup and on-board analysis
  • Non-admin users can run the instrument control software
  • Enhanced security reduces the risk of data being compromised
  • Enhanced user interface within operating system and control software
  • Improved user account credentialing
  • Improved performance compared to earlier Windows versions
  • Windows 10 OS has increased stability and will continue to receive support and security updates

The Upgrade Process

An Illumina field service representative must come on site to do the upgrade. To schedule an upgrade, contact an Illumina field representative. Here’s what to expect with the upgrade:

  • The update to MCS v4 includes installation of a new 1TB solid state drive. To transfer previous data and custom genomes from your current drive to the new drive, save the data to your local network or the cloud prior to MCS v4 installation, then move it to the new drive
  • Your local field service representative may provide you with a pre-upgrade questionnaire to be completed before the upgrade.
  • After the MiSeq system is upgraded to MCS v4, the system cannot revert to previous versions of MCS. MCS v4.0 is Windows 10 based while previous versions of MCS run on Windows 7.
  • Your IT department should be informed and aware of the changes for internal planning purposes.
  • The upgrade should take approximately 3–4 hours.

Local Run Manager

Local Run Manager is upgraded to v3 as part of MiSeq Software Suite v4. For details on what is new with this Local Run Manager release, refer to the MiSeq Software Suite v4.0 Release Notes.

MiSeq Reporter is not supported in MiSeq Software Suite v4. If your system is currently on MiSeq Control Software v2.6 or prior, Local Run Manager v3 will replace MiSeq Reporter.

Local Run Manager v3 includes several new features:

  • Added support for Windows 10. Windows 7 is not compatible with Local Run Manager v3.
  • Decoupled library prep kits and index adapter kits.
  • Security improvements for database account management.
  • Admin password recovery capability.

Local Run Manager Module Availability

If the module you need is not available, you should delay upgrading your system to MCS v4 until the required module is available. For module downloads and more information, see the Local Run Manager Module Selector.

Release Date* Module Version
January 2021 Library QC
February 2021 DNA Amplicon
  DNA Enrichment
2021 (Pending) 16S Metagenomics  
  RNA Amplicon  
  PCR Amplicon  
  RNA Fusion  
  Small RNA  
  Amplicon DS  

*Availability date is subject to change

Admin and Non-Admin Privileges in MCS v4

With MCS v4, non-admin users can run the instrument control software. There are several considerations for non-admin accounts:

  • Accounts that are added to the MiSeq OS need to be managed through customer IT administration for permissions and access.
  • Control software allows only one user to be logged in at a time. For this reason, users should not log out of an account during an active sequencing run, to prevent premature termination of the run.
  • Remote logins (like RDP, SSH, Telnet) should be avoided and/or disabled to avoid premature run termination (same reasons as above).
  • Admin account login will be prompted for certain situations, such as installation of software, including Local Run Manager modules.
  • Only admins will have read/write access to the C: drive; non-admin users will have read-only access.

Compatibility Considerations

  • Sample sheets generated by Illumina Experiment Manager (IEM) are not compatible with Local Run Manager v3. Refer to Local Run Manager Module Selector and select the relevant module for more information and example sample sheets.
  • Currently MiSeq Software Suite v4 does not support custom recipes. For more information contact Illumina Technical Support.
  • The current release of the BaseSpace Clarity LIMS MiSeq integration does not yet support integration with MiSeq RUO running MCS v4 (as of 2/5/21). If this integration is in use, you should delay the upgrade to MCS v4 until an updated integration package is available. Information on integrations can be found on the BaseSpace Clarity LIMS Support page.

Additional Resources