> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0.md).

# NextSeq 500/550 v2.5.0

The Illumina NextSeq 500/550 Integration v2.5.0 includes the following features and functionality:

* New workflow that maps to lab protocols and instrument runs. In NextSeq 500/550 Sequencing v1.3, the [forward-orientation samplesheet](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001800) generated in Dilute and Denature step is now compatible with NextSeq 500/550 Control Software Version 4.2 and Local Run Manager v4.0 for the following modules:
  * Assembly Analysis
  * DNA Enrichment Analysis
  * GenerateFASTQ Analysis
  * Library QC Analysis
  * 16S Metagenomics Analysis
  * PCR Amplicon
  * Resequencing Analysis
  * DNA Amplicon Analysis
  * RNA Fusion Analysis
  * Small RNA Analysis
* Automated generation of the sample sheet. The reverse-complement sample sheet is used with the bcl2fastq2 v2.20.0 analysis software.
* Automated tracking of the NextSeq sequencing runs and parsing of run statistics into Clarity LIMS, which includes the following information:
  * Sequencing run metrics
  * Sequencing run parameters
  * Real-Time Analysis v2 (RTA2) run directory location and other run-specific information
* Preconfigured Library Prep Validation workflow used for validation purposes. This workflow contains a single-step protocol that models the library prep required to produce normalized libraries that are ready for the NextSeq 500/550 Sequencing workflow. The versions of the Library Prep Validation workflow NextSeq 500/550 Sequencing workflow depends on the version of IPP installed (see table above). For more information, refer to [NextSeq 500/550 Integration v2.5.0 User Interaction, Validation and Troubleshooting](/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0/nextseq550-v2.5.0-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 by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/nextseq550/nextseq550-v2.5.0.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

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.