Adapters may dimerize during ligation, which can negatively impact the quality and the usable throughput of the sequencing run. Clusters resulting from adapter dimers tend to generate high signal, resulting in increased crosstalk between adjacent nano wells. Dimers also tend to seed very efficiently due to their small size, further decreasing the number of nano wells available for library clusters.

Additionally, the presence of adapter dimers inflates the library quantitation, so the amount of library loaded does not correlate to the number of library molecules you want to sequence. This can also skew any sample pooling efforts, leading to undesirable differences in the relative representation of pooled libraries.