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Journal Article

HOPS: Automated detection and authentication of pathogen DNA in archaeological remains

MPS-Authors
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Hübler,  Ron
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Key,  Felix Michael
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221103

Warinner,  Christina G.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Bos,  Kirsten I.
CoDisEASe, Max Planck Institute for the Science of Human History, Max Planck Society;
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Krause,  Johannes
MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society;
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons179620

Herbig,  Alexander
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Citation

Hübler, R., Key, F. M., Warinner, C. G., Bos, K. I., Krause, J., & Herbig, A. (2019). HOPS: Automated detection and authentication of pathogen DNA in archaeological remains. Genome Biology, 20(n/a): 280 (2019). doi:10.1186/s13059-019-1903-0.


Cite as: https://hdl.handle.net/21.11116/0000-0004-5F64-2
Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present day environmental or clinical samples, but can also be fruitfully applied to molecular data from archaeological remains (ancient DNA), and a focus on ancient bacteria can provide valuable information on the long-term evolutionary relationship between hosts and their pathogens. Here we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequence data that provides straightforward and reproducible information on species identification and authenticity. HOPS provides a versatile and fast pipeline for high-throughput screening of bacterial DNA from archaeological material to identify candidates for subsequent genomic-level analyses.