# 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](https://emea.support.illumina.com/content/dam/illumina-support/documents/downloads/software/nextseq/nextseq-v4-0-1-software-release-notes-1000000101366-00.pdf)
* Search for Knowledge Base article **Upgrading to NextSeq Control Software v4**

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2375), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002375%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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