SUMMARY: Integration of exogenous DNA into host cell chromatin is a hallmark of many virus and transposon lifecycles and the foundational basis for many modern cellular and genetic therapies. Defining integration sites (ISs) in a population of cells can accordingly inform fundamental aspects of mobile DNA biology and therapeutic treatment outcomes. Here, we describe intmap, a software that generalizes IS analysis to diverse data-types and experimental systems. intmap functions independently of strict library design assumptions and is highly tunable with respect to analysis parameters. Using both simulated and experimental data, we show that IS mapping with intmap is fast, accurate, and highly flexible. AVAILABILITY AND IMPLEMENTATION: intmap, related documentation, and a convenient installation script are available at https://github.com/gbedwell/intmap. Additional information is provided in the online Supplement. Analysis commands, outputs, and other information related to this manuscript are available at https://doi.org/10.5281/zenodo.19475929.