# 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.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                              |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *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)*.* |