> 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/library-preparation/general/library-preparation-general-faq-list/000006091.md).

# Should indexes be read when sequencing a single library?

When sequencing a single library in a run, it is not recommended to perform index reads, as the index read or reads will not be color balanced due to the presence of a single sequence.

* During run setup or when creating a sample sheet in Illumina Experiment Manager or Local Run Manager, enter zero for the index reads.
* All reads will go to the undetermined folder. Sample reads will be separated from PhiX reads (if present) during alignment in the analysis workflow.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #6091), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006091%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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