> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0.md).

# NovaSeq 6000 File-based v2.6.0

The integration includes the following functionality:

* Preconfigured NovaSeq 6000 v2.3 workflow that maps to lab protocols and instrument runs.
* Preconfigured NovaSeq Standard (NovaSeq 6000 v2.3) protocol that supports the loading of pooled libraries into a library tube.
* Preconfigured NovaSeq Xp (NovaSeq 6000 v2.3) protocol that supports individual lane loading on the NovaSeq.
* Automated generation of a sample sheet for use with bcl2fastq2 v2.20 analysis software.
* Automatic generation of run recipe file (JSON format) that is automatically uploaded to the sequencing instrument and used to set up and initiate the run.
* Automated tracking of the NovaSeq sequencing run and parsing of run statistics (per run per lane) into Clarity LIMS, including:
  * Progress and metrics of sequencing run
  * Per instrument sequencing runs (tracked as part of the Run ID field value)
  * Sequencing run parameters
  * Real-Time Analysis v3 (RTA3) run directory location and other run-specific information
* Preconfigured NovaSeq Validation Library Prep (NovaSeq 6000 v2.3) workflow used for validation purposes only. The workflow contains a single-step protocol that models the library prep required to produce normalized libraries that are ready for the NovaSeq 6000 v2.3 workflow. For details, refer to [NovaSeq 6000 Integration v2.6.0 User Interaction, Validation and Troubleshooting](/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0/novaseq6k-file-v2.6.0-user-interaction-validation-and-troubleshooting.md).


---

# 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://help.connected.illumina.com/clarity-lims/instruments-and-integrations/novaseq6k-file/novaseq6k-file-v2.6.0.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.