What are the peaks around 70 – 90 bp in addition to the main library peak on a fragment analyzer trace?

Peaks from 70 – 90 bp (see the trace below) are primer dimers from the 2^nd PCR that result from incomplete removal of small molecular materials during the final magnetic bead purification. These are usually caused by inaccurate pipetting of magnetic beads volume, poor mixing prior after adding magnetic beads, and/or incomplete removal of supernatant and ethanol during washing steps. If these peaks are significant, one can pool all indexed libraries (that will be sequenced in the same lane) and perform one additional round of 1.2X magnetic bead purification, before the quantification step prior to sequencing.