> 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/other-release-notes/miseqdx-v1.5.0-release-notes.md).

# MiSeqDx v1.5.0

* MiSeq Operating Software (MOS) v1.1.7
* Real-Time Analysis (RTA) v1.16.18
* MiSeq Reporter Software (MRS) v2.2.31.1

## Features to note for this release

The **Illumina MiSeqDx Integration Package v1.5** includes support for both MiSeqDx **Research** mode and **Diagnostic** mode.

* For **Diagnostic** mode, this integration package supports the following three kits: **CF 139-Variant Assay, CF Clinical Sequencing Assay**, and **Universal Kit.**
* For **Research** mode, the **Illumina MiSeq Integration Package v5.3** is also included.

## New features

This release supports the integration between BaseSpace Clarity LIMS and the MiSeqDx instrument. At a high level, this integration includes the following features:

* In **CF 139-Variant Assay** and **Universal Kit** workflows, indexes are automatically placed on samples when running the **PCR Amplification** step in the **Library Prep** protocol.
* Key metrics are parsed back into LIMS following the completion of primary analysis on the instrument.
* Variant call files are attached to the **Variant Calling** step in the LIMS, individually for each sample and one combined file for all the samples together.

## Defects fixed

None

## Known issues

This release contains the following known issues, which are prioritized for a later release:

* Following a sequencing run, user must wait until the run report is automatically generated and attached before finishing the **MiSeqDx Run** step. If user completes the step before these events occur, they cannot return to the step and regenerate the report.
* The metrics parsed back into the LIMS for %Bases Q30 R1 and R2 are not consistent with Sequencing Analysis Viewer.


---

# 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/other-release-notes/miseqdx-v1.5.0-release-notes.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.