> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001318.md).

# How to set up a PhiX validation run with Local Run Manager

A PhiX validation run confirms proper hardware and software performance of the instrument. The Illumina PhiX control library is a well-balanced genome with relatively equal representation of A, C, G and T nucleotides. Standard PhiX lacks indexes and is not an appropriate tool for assessing index read performance.

PhiX validation runs can be set up on instruments with the Local Run Manager software suite bundled for on-instrument use. These instruments are the iSeq 100; MiSeq with MiSeq Control Software v3 and v4; NextSeq 500/550 with Control Software v4; and MiniSeq. Please note that while different control software versions will be running slightly different versions of the Local Run Manager, the run setup process for a PhiX run is the same.

1. Launch the Chromium browser and enter <http://localhost/#/login> in the address bar. If required, enter the user ID and password.

![](/files/LZuIkzfQtoHfEv7GZaRO)

2. Select **Create Run** and choose **Generate FastQ** from the drop-down list.

![](/files/a4cynIpo05GrGAmpOrVI)

3. Enter the following values in the highlighted fields:

*

```
* **Run Name**: PhiX validation run
```

```
* **Library Prep Kit**: Custom
* **Index Reads**: 0 (**Note:** PhiX is unindexed and selecting 1 or 2 Index reads can cause the run to terminate prematurely)
* **Read Type:** Paired End
* **Read Length:** Enter at least 26 cycles for each read (or follow Illumina Support guidance on the number of cycles for each read)

![](/files/j9ZT6D7RRjSsxy8c7l5U)
```

4\. Keep default values in the **Module-Specific Settings** field.
5\. Scroll to the bottom of the Create Run page. In the Import Samples table, type PhiX in the **Sample ID** field.
6\. Select **Save Run**.

![](/files/KI1pHD0HPPDw9QVrqq4i)

7. Close the browser window and return to the instrument Control Software.
8. Select the **Local Run Manager** run setup option and then select ‘**PhiX validation run**’ from the list of available runs and proceed to sequencing.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1318), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001318%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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