Hybridization capture (also called enrichment) is a molecular technique used to focus high-throughput sequencing effort to a targeted region (or regions) of the genome, thereby reducing costs. This method has been used with great success in a wide range of research topics, including applied conservation genetics, and has been the subject of many studies aiming to optimize and improve the technique. In such technical optimization studies, it is common to minimally sequence (i.e., shallow sequencing) experimental capture libraries to save costs, and evaluate hybridization capture efficiency at lower sequencing effort than would be necessary for downstream analyses. Here I use simulations to show how this practice can produce misleading results and, ultimately, non-optimal experimental design choices. I argue that hybridization capture optimization studies must investigate their experiments at variable sequencing efforts and evaluate results in the context of the required target-space coverage for downstream analyses.

杂交捕获（也称为富集）是一种分子技术，用于将高通量测序工作集中在基因组的一个（或多个）目标区域，从而降低成本。这种方法已在广泛的研究课题中取得巨大成功，包括应用保护遗传学，并且已成为许多旨在优化和改进该技术的研究的主题。在此类技术优化研究中，通常对实验捕获文库进行最低限度的测序（即浅层测序）以节省成本，并以比下游分析所需的测序工作量更少的测序工作量评估杂交捕获效率。在这里，我使用模拟来展示这种做法如何产生误导性结果，并最终导致非最佳实验设计选择。