Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusHunter, for the identification of viruses and their integration sites in host genomes using any type of existing NGS data. VirusHunter's unique features include the characterization of insertion loci of any type of virus in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline.