input amount depends on a number of factors, including the number of reads devoted to a sample, the use of targeted DNA capture, genome and target size, and gene and target copy number. We formally outline the relationship between these parameters and provide the optimal DNA input amounts to maximize the final amount of data. Finally, we have included the option to use targeted DNA capture, which greatly expands the utility of DS beyond small, highly pure genomes, such as mtDNA and other small plasmids that were presented in our original publication.