PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data
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…
Ancient DNA analysis has unveiled a wealth of pathogens spanning various time periods, host species, and material origins. Nevertheless, current palaeogenomic pipelines primarily concentrate on human host screenings, lacking microbial screening techniques. We introduce PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically tailored for the initial screening and subsequent detection of pathogens in shotgun sequencing data derived from ancient animal remains.
PIGSTI's Snakemake workflow encompasses host detection, genome mapping, and pathogen identification, yielding outputs fitting for population genetics and phylogenetic analyses. Upon testing on 952 recently sequenced and publicly accessible animal palaeogenomic datasets, we detected approximately 15 ancient zoonotic and animal pathogens with high accuracy.
Among these, we documented the earliest instances of Rickettsia felis and Leptospira borgpetersenii in ancient animal specimens. These findings underscore PIGSTI's value in assessing pathogen diversity within ancient animal hosts and piecing together historical host-pathogen associations.
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