# IDT for Illumina DNA/RNA Unique Dual Index Compatibility on the MiniSeq

IDT for Illumina DNA/RNA Unique Dual Indexes are 10 bp each.

Currently the MiniSeq Reagent Cartridges are not able to complete dual 10 bp index reads without also reducing the insert read lengths to compensate for the additional index cycles.

* In order to sequence the dual 10 bp indexes on the MiniSeq, set up the run with four fewer sequencing cycles, either 151+10+10+147 or 149+10+10+149.
* For FASTQ Generation, Illumina recommends upgrading to MiniSeq Control Software v2.0 which has Local Run Manager 2.0
  * If the MiniSeq has Local Run Manager v1.3.1, add the definition files for the index kits used by adding a custom library prep kit. The definition files are available on the IDT for Illumina UD Indexes Support Page [here](https://support.illumina.com/sequencing/uniquedualindex.html).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                              |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #2045), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002045%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: 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:

```
GET https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000002045.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
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.