Software information regarding the NCS 4.0.X upgrade for NextSeq 500/550

What are the changes?

The changes include both hardware and software changes.

Software and firmware changes:

• For Research Use Only (RUO)

  • Supports v2.0 and v2.5 Reagents (2.0 reagents will be discontinued)

  • Reintegration of Win10 system in Customer’s Network

  • Not backwards compatible to Windows 7 or NCS <2.2.x

  • Includes Local Run Manager (LRM) Genomes but NO LRM MODULES pre-installed

• Infinium MethylationEPIC scanning on NextSeq 550 instruments

• Integration of Local Run Manager (LRM v2.2.1)

  • BaseSpace PrepTab no longer compatible

  • Manual and LRM modes, both have BaseSpace Sequence Hub (BSSB) Monitoring/Analysis options

  • LRM 2.x Modules available

• Improved Illumina Proactive

  • Additional metrics sent to Illumina Proactive

• Real Time Analysis (RTA) v2.11.3

  • Phasing/ PrePhasing Values calculated through all cycles

  • Sequencing Analysis Viewer (SAV) will typically show “elevated” values compared to previous NextSeq Control Software (NCS) versions. This is normal. ~+0.1% Phasing, +~0.08% PrePhasing

Hardware changes:

• Airflow retrofit upgrade (Selected instrument) (Engineer visit required)

  • Requires running FTS if installing the Airflow retrofit upgrade

  • Roughly ~4 days including software upgrade & validation

  • Airflow retrofit will not function without software v4.0 upgrade

  • Retrofit entails Main Board (MPCA) swap, new fans, new chassis/skin, new air filter, Image Module (IM) cleaning and NCS 4.0 Update procedure (New drives, firmware)

  • LED measurement will be taken before (on original Software) and after (on v4.0 software)

  • Air filter needs to be replaced every 3 months

• To install 2 hard drives (Each 2TB in RAID 1 Array) (Engineer visit required)

  • Windows 10 Images and NCS Suite pre-installed on drives (Windows 10 Enterprise LTSC)

Additional Resources:

• NextSeq Software Release Notes

• Search for Knowledge Base article Upgrading to NextSeq Control Software v4

For any feedback or questions regarding this article (Illumina Knowledge Article #2375), contact Illumina Technical Support [e-mail].