The free Polyidus software identifies the exact genomic regions for integration of a known virus. We developed Polyidus to identify viral integration sites with chimeric sequencing reads from any paired-end sequencing data. First, Polyidus aligns reads to a viral genome. It allows for partial mapping using local alignment, and removes any sequencing fragment where neither read maps to the virus. Second, Polyidus aligns the selected reads to the host genome, permitting partial mapping. Third, Polyidus identifies chimeric reads: those reads mapped partially to the host genome and partially to the virus genome. Fourth, for each chimeric read, Polyidus reports the start and strand of integration in both the host and viral genomes. Polyidus also reports the number of chimeric reads supporting each integration site. In the previous version, we called our software Bellerophon. After noticing that the name was previously used for another software, we changed the name to Polyidus. Update on version 1.1.0: The host BAM file for paired-end analysis was expected to be sorted by reads, but was in fact sorted by position. The bug is fixed in v1.1.0