The rate of PCR duplicates correlates notably with the amount and quality of the provided sample material. However, with our optimized and fully automated library preparation process with sample type dependent DNA input and limited number of PCR cycles we increase library complexity and deliver the lowest possible PCR duplicate rate out of the provided DNA sample.
In addition, due to the patterned flow cell used for HiSeq4000 and NovaSeq6000 sequencers, the rate of PCR duplicates may be increased by technical duplicates.
If you order Bio-IT analyses of your samples (e.g. SNP identification) only one copy of the duplicate read pair is kept in the alignment. The remaining duplicates are excluded from further analysis to prevent bias.