The study of parasitic species can shed light on aspects of their host’s ecology. Such interactions are however often unknown or understudied due to the difficulty to detect and/or quantify many infections. Whole-genome sequencing and re-sequencing data have been generated at an increasing rate and reduced costs over the last two decades. Projects based on whole organisms, like whole insect specimens, provide genomic material for the target taxon, but may also include sequencing reads from associated microbes and other parasites. Here, we screened for the presence of non-host reads in a collection of whole-genome (re-) sequence projects from the Glanville fritillary butterfly, Melitaea cinxia, a model organism in research on the ecology and evolution of species in spatially structured and fragmented landscapes.