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, and can, in some instances, lead to run failure. If the run includes the single library and phiX, the phiX reads will be removed at the data alignment step. Alternatively, reads aligning to phiX can be bioinformatically removed prior to analysis of sample data.

• Note: phiX is an unindexed library and cannot be used to add base diversity to index reads.

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