> 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/miseqdx/miseqdx-v1.10.0.md).

# MiSeqDx v1.10.0

The Illumina MiSeqDx Integration v1.10.0 includes the following features:

* MiSeqDx RPM that supports Diagnostic (Dx) mode.
* MiSeq RPM that supports Research (RUO) mode.
* Preconfigured Clarity LIMS protocols that map to library prep and sequencing lab protocols and instrument runs.
* Preconfigured protocols that allow for validation of the sample sheet generation and index placement functionality.
* Automatic generation of:
  * A sample sheet file for use with the MOS (Diagnostic mode) instrument software.
  * A run report, which includes the current run statistics.
* Automated tracking of the following information in Clarity LIMS:
  * Progress and metrics of a MiSeqDx sequencing run
  * Per-instrument sequencing runs
  * Sequencing run parameters
  * Real-Time Analysis (RTA) run directory location and other run specific information
* The ability to monitor the run status (cycle number) across multiple instruments from within Clarity LIMS.
* The ability to attach Variant Call Format (VCF) files to Clarity LIMS.


---

# 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/miseqdx/miseqdx-v1.10.0.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.
