Frequently asked questions about upgrading to NextSeq Control Software version 4.0


Improvements have come to NextSeq Control Software (NCS). Version 4.0 has been introduced for NextSeq 500/550 and NextSeq 550Dx (in Research Use Only [RUO] mode) instruments. The upgrade includes the installation of Local Run Manager (LRM), greatly simplifying run setup and increasing the onboard analysis capabilities of these Illumina sequencing systems.

NextSeq Control Software (NCS) New Features Include:

  • Scanning of Infinium MethylationEPIC BeadChips on instruments with array capability
  • Windows 10 compatibility: Initially, the NextSeq 500/550 operated with Windows 7, which was obsolesced by Microsoft at the end of 2019
  • Enables the use of the NextSeq 500/550 v2.5 kit in Research Use Only (RUO) mode on the NextSeq 550Dx instrument
  • 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 (LRM)
    • Introduction of onboard analysis options
    • Improved interface for configuring run and entering sample information

Frequently Asked Questions:

Are the installers for NCS version 4.0 available to download online?

  • No, the update must be performed by an Illumina engineer as the update requires installation of new hard drives or reimaging of the system. Please contact for questions and scheduling the update.

What are the benefits of Local Run Manager 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.

Is Prep Tab required when uploading runs to BaseSpace for analysis?

  • LRM replaces Prep Tab. Prep Tab is incompatible with the NCS 4.0 and will not be included in the latest version.

Is BaseSpace Onsite (BSO) compatible with the NCS v4.0 upgrade?

  • With the upgrade to NCS suite v4.0, BSO is no longer able to communicate directly with the NextSeq instrument. LRM replaces the run setup and analysis features of BSO. More details regarding the LRM analysis modules are found here.
  • Support for BSO ended in 2019. While support for the interconnection between BSO and NCS suite v4.0 is not supported, BSO can still be used by customers.
  • Note: there are several options available to customers using BSO devices:
    • BSO accepts FASTQ file outputs from LRM. The FASTQ outputs from LRM can be uploaded to BSO using the FASTQ import capabilities.
    • BSO can be repurposed with a Windows 10 license and configured either to store output files from the NextSeq instrument or to run LRM off-instrument, which allows analyses of NextSeq runs. The latter option is helpful for high-throughput sequencing, and labs with multiple benchtop sequencers.
    • BSO can be repurposed with a Linux Operating System. This option allows customers to configure BSO to store runs from the NextSeq instrument and utilize Illumina® analysis tools, and other open-source analysis tools.

Contact with questions regarding the options available for using BSO with NCS v4.0.

Is the instrument connected to Illumina Proactive after the upgrade?

  • Illumina Proactive settings are retained after the upgrade. If you would like to make changes to 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 drives with Windows 10 OS are installed with the upgrade.

How do I schedule my upgrade?

  • NCS v4.0 is now shipping on new NextSeq 500/550’s. Contact to request the software upgrade to NCS v4.0 on installed NextSeq 500/550 instruments.

Additional resources