MiniSeq Software Suite v2 Upgrade

The MiniSeq Software Suite upgrade provides several enhancements to MiniSeq systems, including:

  • Windows 10 operating system upgrade from Windows 7
  • Feature updates to Local Run Manager Software

The following software updates are included in the MiniSeq Software Suite v2 upgrade:

Software Application Prior Version New Version
Operating System Windows 7 Windows 10
MiniSeq System Suite Installer 1.1.8 2.0
MiniSeq Control Software (MNCS) 1.0, 1.1 2.0
MiniSeq Service Software (MNSS) 1.0, 1.1 2.0
MiniSeq Real Time Analysis (RTA) 2.8.6 2.11.4
MiniSeq Recipe Installer 1.0.0 2.0
Universal Copy Service (UCS) None 1.6.3
BaseSpace Broker 2.9.1 Replaced by UCS v1.6.3
Run Copy Service 1.0.20 Replaced by UCS v1.6.3
Illumina DMA Driver 4.5.3 4.5.3
Local Run Manager 1.3.1 2.4.1

The Upgrade Process

An Illumina Field Service Engineer 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:

  • No specific preparation is necessary, although your IT department should be informed and aware of the changes for internal planning purposes.
  • The MiniSeq system hard drive will be replaced.
  • After the MiniSeq system is upgraded to MNCS v2, the system cannot revert to previous versions of MNCS. MNCS v2 is Windows 10 based while previous versions of MNCS run on Windows 7.
  • The upgrade should take approximately 3–4 hours.

Admin and Non-Admin Privileges in MNCS v2

With MNCS v2, non-admin users can run the instrument control software. There are several considerations for non-admin accounts:

  • Accounts that are added to the MiniSeq OS will 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.

Local Run Manager

Local Run Manager is upgraded to v2 as part of MiniSeq System Suite Installer v2. For details on what is new with this Local Run Manager release, refer to the MiniSeq System Suite Release Notes on the support website. If you need to continue to use Local Run Manager v1, you cannot upgrade your system to MNCS v2.


Local Run Manager v2 includes several new features:

  • Full HTTPS support for security enhancements
  • Integration with Illumina Proactive to send instrument performance data
  • Improved file copy process
  • Support for local machine accounts (Local Run Manager framework v2.4 and later)
Analysis Modules Compatibility

Local Run Manager v2 is compatible with the latest Local Run Manager Analysis Modules release, available for download from the support website.

Local Run Manager Module Version
16S Metagenomics 1.0
Amplicon DS 2.0
Assembly 1.0
DNA Amplicon 2.1
DNA Enrichment 2.0 (not compatible with 1.0)
Generate FASTQ 2.0
LibraryQC 1.1, 1.0
PCR Amplicon 1.0
Resequencing 2.0
RNA Amplicon 2.0
RNA Fusion 2.0
Small RNA 2.0
Retaining Legacy Data

The update to MNCS v2 includes installation of a new hard drive. To transfer Local Run Manager data from your current drive to the new drive, save the data to your local network or the cloud prior to v2 installation, then move it to the new drive.

Setting Up a Run Remotely

If you have previously used BaseSpace Sequence Hub Prep tab to set up a run remotely, you can now use Local Run Manager for this task. For details, refer to the Viewing Local Run Manager section of the Local Run Manager Software Guide.

Additional Resources