# 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).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #5574), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005574%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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