Reconditioning PCR for removal of PCR bubbles in Illumina librarys v1

This protocol describes how to remove partly single-stranded PCR products ("PCR bubbles") from Illumina libraries. For more information about this phenomenon please see this explanation from Illumina. For metabarcoding libraries, it can be hard to estimate the optimal input template or the perfect amount of PCR cycles and therefore overamplification happens frequently. PCR bubbles cannot be quantified reliably with fluorometric-based methods and may look different on different capillary electrophoresis devices. PCR bubbles can lead to failed sequencing runs due to over- or underloading the flowcell.