Revision History

Document

Date

Description of Change

Material # 20006831

Document # 15069765 v08

June 2023

Renamed document to NextSeq 500 and NextSeq 550 Sequencing Systems Product Documentation.

Reorganized steps in Prepare the Flow Cell section.

Clarified that scratches and minor cosmetic defects are safe to use in the Prepare the Flow Cell section.

Removed the requirement of a quick wash after a shutdown.

Removed Local Run Manager instructions.

Updated User-Supplied Consumables and Equipment section with new air filter PN 20063988, replaced PN 20022240.

Material # 20006831

Document # 15069765 v07

October 2021

Update the maximum run length to Sequencing Run Duration.

Updated Number of Cycles in a Read section.

Reorganized steps in Prepare the Flow Cell section.

Included new and legacy cartridges in manual.

Included 3 spare air filters in Replace Air Filter section.

Updates to System Check section include LRM credentials.

Material # 20006831

Document # 15069765 v06

June 2019

Added workgroup information for BaseSpace Sequence Hub during run set up.

Added UNC path information for the output folder.

Added troubleshooting for network storage errors.

Clarified that air filter directions are for instruments with a filter accessible from the rear panel.

Updated location of files that were in the root folder to run specific folders of the output folder.

Material # 20006831

Document # 15069765 v05

December 2018

Updated software descriptions, screens, and workflow for NextSeq Control Software (NCS) 4.0.

Updated the following additional information for NCS 4.0.

• Added information on Local Run Manager software.
• Updated BaseSpace information to BaseSpace Sequence Hub. BaseSpace Prep tab and BaseSpace Onsite are no longer available.
• Added instructions on selecting Local Run Manager or manual run mode. Manual mode replaces standalone mode, with some modifications.
• Added option to check for instrument software updates in BaseSpace Sequence Hub.
• Added Local Run Manager, Universal Copy Service, and Direct Memory Access driver to the description of the System Suite bundle. Removed BaseSpace Broker and SAV.
• Run Copy Service is now Universal Copy Service.
• Added option to enable custom recipes when loading the reagent cartridge.
• Removed the description of the flow cell image when monitoring run progress.
• Removed the select start-up option for kiosk and Windows mode.
• Added MethylationEPIC v1.0 as a compatible BeadChip type.
• Added maintenance instructions for instruments with an air filter.
• Added new icons for attention, information, and minimizing NCS.
• Updated instructions for customizing run settings and system settings.
• Updated send instrument performance data option.
• Updated data transfer icons.
• Clarified that for scanning, files queued for transfer have no time limit.
• Corrected references of BSM to Buffer Straw Mechanism in motion checks information.
• Added six-month Windows password expiration information.

Added reagent or spectrophotometric-grade methanol or isopropyl alcohol (99%) for instrument maintenance.

Material # 20006831

Document # 15069765 v04

May 2018

Added support for NextSeq v2.5 reagents.

Updated storage/shipping information for NextSeq v2.5 Reagent Kits shipping flow cells at ambient temperatures. NextSeq v2.5 flow cells continue to require previous storage conditions.

Added information about NextSeq v2.5 Reagent Kits requiring software updates to version 2.2.

Added note regarding mid output kit loading concentration.

Added note regarding saving flow cells.

Added note recommending that high output flow cells are used for system checks.

Material # 20006831

Document # 15069765 v03

March 2018

Removed the default user name and password required to log on to the operating system. Illumina recommends using site-specific credentials.

Added information about the Illumina Proactive monitoring service in the Select BaseSpace Configuration section.

Updated RTA v2 software references to RTA2.

Material # 20006831

Document # 15069765 v02

March 2016

Added section titled Indexing Considerations.

Removed steps to inspect the flow cell.

Specified loading volume and concentration in the step to Load Libraries onto the Reagent Cartridge.

Material # 20001843

Document # 15069765 v01

October 2015

Specified that an equivalent to the recommended supplier of NaOCl is a laboratory-grade equivalent.

Added recommendation for annual preventive maintenance service.

Reorganized information in the Overview and Getting Started chapters. Added instructions for customizing system settings.

Removed Live Help instructions from troubleshooting chapter. This feature was removed from the control software.

Part # 15069765 Rev. B

May 2015

Corrected description of reserved reservoirs on the reagent cartridge.

Part # 15069765 Rev. A

May 2015

Initial release.