If you are sequencing a low complexity library (e.g. a PCR-amplicon library) using Illumina sequencers, it's a good idea to spike in some PhiX to improve base quality, as explained here and here on the Illumina support pages. On the seqanswers forum they say that PhiX is used for:
"introduction of sequencing diversity in low-complexity libraries
(diversity is needed to discriminate clusters and create signal
thresholds for base-calling). As the software has improved, the
recommended amount of phiX spike-in has decreased."
Another comment says:
"Older basecalling software on the MiSeq used to require a 50% phiX spike
for low-diversity (amplicon samples). More recently, the software has
been updated and only requires a 5-10% spike."
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