Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes"

We clarify the design principles and evaluation choices underlying Syotti, a robust and scalable probe-design tool developed to support large, heterogeneous bacterial datasets with minimal parameter tuning. We highlight Syotti's ability to perform simultaneous large-scale designs and its effectiveness as a reliable alternative when existing tools such as CATCH are not well suited to the problem setting.