# Should index reads be performed if only one library is being sequenced?

**Should index reads be performed if only one library is being sequenced in a run?**

Illumina does not recommend performing index reads when one library is sequenced alone, as the index read(s) will be low in base diversity and this can negatively impact the sequencing performance, and can, in some instances, lead to run failure. If the run includes the single library and the phiX control v3 (note: this is not the indexed phiX control, catalog 20151542), the phiX reads will be removed at the data alignment step. Alternatively, reads aligning to phiX can be bioinformatically removed prior to analysis of sample data.

* **Note**: phiX is an unindexed library and cannot be used to add base diversity to index reads.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                              |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #6541), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006541%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-faq-list/000006541.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.