Large‐scale double‐digest RAD sequencing (ddRADseq) datasets generated for genotyping are increasingly available in aquaculture, yet their unmapped reads remain largely unexplored for pathogen surveillance. Here, we evaluated the utility and limitations of repurposing unmapped ddRADseq reads to examine pathogen‐associated and disease‐associated microbiome‐pathobiome patterns during scale drop disease (SDD) outbreaks in farmed...