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

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...

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Autores principales: Hübler, Ron, Key, Felix M., Warinner, Christina, Bos, Kirsten I., Krause, Johannes, Herbig, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913047/
https://www.ncbi.nlm.nih.gov/pubmed/31842945
http://dx.doi.org/10.1186/s13059-019-1903-0
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author Hübler, Ron
Key, Felix M.
Warinner, Christina
Bos, Kirsten I.
Krause, Johannes
Herbig, Alexander
author_facet Hübler, Ron
Key, Felix M.
Warinner, Christina
Bos, Kirsten I.
Krause, Johannes
Herbig, Alexander
author_sort Hübler, Ron
collection PubMed
description 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.
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spelling pubmed-69130472019-12-30 HOPS: automated detection and authentication of pathogen DNA in archaeological remains Hübler, Ron Key, Felix M. Warinner, Christina Bos, Kirsten I. Krause, Johannes Herbig, Alexander Genome Biol Method 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. BioMed Central 2019-12-16 /pmc/articles/PMC6913047/ /pubmed/31842945 http://dx.doi.org/10.1186/s13059-019-1903-0 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Hübler, Ron
Key, Felix M.
Warinner, Christina
Bos, Kirsten I.
Krause, Johannes
Herbig, Alexander
HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title_full HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title_fullStr HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title_full_unstemmed HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title_short HOPS: automated detection and authentication of pathogen DNA in archaeological remains
title_sort hops: automated detection and authentication of pathogen dna in archaeological remains
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913047/
https://www.ncbi.nlm.nih.gov/pubmed/31842945
http://dx.doi.org/10.1186/s13059-019-1903-0
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