HOPS: automated detection and authentication of pathogen DNA in archaeological remains
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13059_2019_Article_1903.pdf
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Author(s)
Hübler, Ron
Key, Felix M
Warinner, Christina
Bos, Kirsten I
Krause, Johannes
Herbig, Alexander
Date Issued
December 16, 2019
Journal
Genome Biology
Publisher
BioMed Central
Citation
Hübler, Ron et al. "HOPS: automated detection and authentication of pathogen DNA in archaeological remains." Genome Biology 20 (Dec. 2019): 280 doi 10.1186/s13059-019-1903-0 ©2019 Author(s)
Version
Final published version
Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s13059-019-1903-0
