> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-faq-list/000005574.md).

# 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).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *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)*.* |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://knowledge.illumina.com/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-faq-list/000005574.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.