All libraries must pass a strict 3-step quality control process before they are loaded into the sequencer. The first step is quantification with Qubit to obtain the concentration in ng/ul. The second step is running the library in a Bioanalyzer to find out the size distribution. With concentration and average size, we calculate the molar concentration (in nM) which gives an idea of the number of molecules in the library. The final QC step is quantification via qPCR; this qPCR uses specific primers that bind to the ends of the adapters (P5 and P7 in the case of Illumina), so only the fragments that contain both adapters are amplified and read. When multiple libraries are going to be pooled together for sequencing, we run Qubit and Bioanalyzer on all of the libraries, then pool them equimolarly, and we finally quantify the final pool with qPCR.
The Core charges a $200 library QC fee, for batches of up to 11 libraries, and includes the pooling step when the libraries are prepared at the Core. This fee is charged for all libraries that are going to be sequenced.