This document provides users with a complete set of protocols that encompass all Covaris Adaptive Focused Acoustics^® (AFA^®) instruments for DNA shearing to 150 to 200 bp with 50 to 55 μl of sample volume, to be readily compatible with the Agilent SureSelect Target Enrichment System (XT or XT2). The goal is to provide the most precise, pre-validated protocols to ensure the best outcome and compatibility for library preparation and subsequent sequencing applications.