The use of next-generation sequencing (NGS) has become the standard for research projects in genomics. There is a pressing need for automating all steps of sample manipulation for NGS from sample plating to library preparation to the final pooling before loading the sequencing instruments. Most of the steps are easily automatable; however, the size selection step which is crucial for many applications is more challenging. While most purification steps can be performed using Beckman Coulter’s SPRI beads, many NGS applications require a tight distribution of fragments within a specific range. This cannot easily be achieved using Beckman Coulter’s AMPure XP beads and size selection on agarose gel is not amenable to high throughput. Double size selection using SPRIselect beads can yield very tight fragment size distributions and is fully automatable in a 96-well format.