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.

For any feedback or questions regarding this article (Illumina Knowledge Article #6091), contact Illumina Technical Support [e-mail].