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
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
- Improved Real Time Analysis (RTA) version
for improved base calling accuracy
- Enhanced Illumina
Proactive monitoring capabilities for increased instrument
- Integration of Local Run Manager (LRM)
- Introduction of onboard analysis options
interface for configuring run and entering sample
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 email@example.com for questions and scheduling the
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
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:
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
- 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 firstname.lastname@example.org 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 email@example.com to request the
software upgrade to NCS v4.0 on installed NextSeq 500/550