Nucleotide diversity is the equal proportions of A, C, G and T nucleotides at each base composition in a sequencing library.
Illumina platforms require sufficient nucleotide diversity for effective template generation.
Sequencing a low diversity library is challenging, but can be accomplished by introducing a proportional amount of spike-in PhiX control in the library prior to the denaturation step. The lower the nucleotide diversity, the more spike-in PhiX control will be introduced into the library. The purpose is to balance the diversity of your library using the PhiX control. Another alternative is to use a well balanced library to spike-into the low diversity nucleotide libraries.
At the end, your library will be sequenced with optimal QC30 scores and higher percentage of passing filter reads. You will also see a percentage of PhiX control reads in the sequencing results that easily can be filtered out during data analysis.
Click here for more technical information from Illumina.