PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Abstract

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.