When should I remove adapter dimers? What protocol do you recommend?

Adapter dimers should be removed when they comprise >5% of your library (i.e. % Integrated in trace is less than 5%), as determined by TapeStation or Bioanalyzer.

Adapter dimers can be removed by gel purification using the QIAquick Gel Extraction Kit (Qiagen 28704) or similar. It is recommended to gel purify the entire multiplexed library pool rather than gel-purifying individual libraries.

Gel purify DNA between 200-700 bp and cleanup as per manufacturer’s instructions. Reassess concentration and fragment distribution and proceed to sequencing. Additional reading about adapter dimers and library prep can be found in the CUTANA™ Library Prep Kit manual.