# Using custom sequencing recipes on Illumina NovaSeq X Series instruments

Custom sequencing recipes are sometimes used for specific sequencing applications; these recipes introduce changes to the standard imaging and/or chemistry steps performed by the sequencer. Illumina does not guarantee performance for runs performed with third party custom recipes.

**Run Setup using a custom recipes on Illumina NovaSeq X Series**

1. Transfer the Custom Recipe files to the Downloads directory on the NovaSeq X Series instrument.

* Note: if using a USB device to transfer the custom recipe, for instruments running Control Software v1.3.1, see Knowledge Base article [Validated USB Storage Devices for NovaSeq X Series Control Software v1.3.1](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000009577) for approved USB external storage devices.

2. In the **Files** application, navigate to the `Downloads`directory.
3. If the files are compressed, right-click on the compressed Custom Recipe files and select **Extract Here**...
   1. Note that the uncompressed Custom Recipe files extract to a sub-directory within `Downloads`. Navigate to this sub-directory within `Downloads` in **Step 7**.
4. Within the NovaSeq X Series Control Software, select the **Start** button, then select **Sequencing**, and choose the appropriate **Side**(**s**) to begin Run Setup.
5. Toggle to **Manual** setup, then confirm that **Manual Run** (**generate BCLs Only**) is selected.
6. Input Run Name and cycle number information.
7. Under the **Review your run information** UI, click **Select**... under **Custom Recipe** (**Optional**) and browse to the uncompressed Custom Recipe file within the `Downloads` directory, then click the blue **Select** button.
8. Select **Load consumables** and proceed with run setup.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                         |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #10171), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009577%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |