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

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. bioRxiv. doi:10.1101/534198.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-5F64-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-5F6A-C
Genre: Journal Article

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 Creators:
Hübler, Ron1, Author              
Key, Felix Michael1, Author              
Warinner, Christina G.1, Author              
Bos, Kirsten I.1, 2, Author              
Krause, Johannes1, 3, Author              
Herbig, Alexander1, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2CoDisEASe, Max Planck Institute for the Science of Human History, Max Planck Society, ou_3033585              
3MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541699              

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Free keywords: ancient DNA, archaeogenetics, pathogen detection, metagenomics
 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.

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Language(s): eng - English
 Dates: 2019-02-07
 Publication Status: Published online
 Pages: 32
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1101/534198
Other: shh2333
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Title: bioRxiv
Source Genre: Journal
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Publ. Info: Cold Spring Harbor Laboratory
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