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. If the run includes the solo library and phiX, the phiX reads will be removed at the alignment step. Alternatively, reads aligning to phiX can be bioinformatically removed prior to analysis of sample data.

For any feedback or questions regarding this article (Illumina Knowledge Article #6541), contact Illumina Technical Support [e-mail].