Run setup modes for the NextSeq 500/550

The NextSeq 500/550 run setup modes available depend on the version of the Windows operating system, and NextSeq Control Software (NCS) installed.

(Terms: LRM = Local Run Manager / BSSH = BaseSpace Sequencing Hub)

Windows 7 with NCS v2.2 or lower\*

Standalone Mode

• Set up the run in the control software.

• BSSH is not used. The data output of the run is only bcls; use bcl2fastq for FASTQ generation.

Prep Tab in BSSH

• If using BSSH for analysis (FASTQ generation, etc.), the run must be planned in Prep Tab.

\*LRM is not available on Windows 7-based systems.

Toggle between modes in Control Software (Manage Instrument / System Configuration).

Windows 10 with NCS v4+ and LRM v2

LRM Mode

• Create the run in LRM.

• The run can also be sent to BSSH.

Manual Mode

• Set up the run in the control software.

• A sample sheet is required if uploading the run to BSSH.

Toggle between modes during run setup (after selecting Sequence).

For any feedback or questions regarding this article (Illumina Knowledge Article #5574), contact Illumina Technical Support [e-mail].