We recommend using the KAPA library quantification kit for Illumina from KAPA Biosystems to measure the concentra-tion of the library. This is a qPCR-based method, using primers that are specific for the Illumina indices. It contains a set DNA standards of a known concentration to measure the exact amount of functional library in your library. The input for the MiSeq needs to be determined accurately to achieve an optimal cluster density.
It is not necessary to quantitate each individual library when they are made within the same NGSgo workflow.
At the end of the library preparation, all samples are pooled together. This single library pool can then be quantified by qPCR.
