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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.