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...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central
2020
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| Online Access: | https://hdl.handle.net/1721.1/126318 |
| _version_ | 1826208579440345088 |
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| author | Hübler, Ron Key, Felix M Warinner, Christina Bos, Kirsten I Krause, Johannes Herbig, Alexander |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science Hübler, Ron Key, Felix M Warinner, Christina Bos, Kirsten I Krause, Johannes Herbig, Alexander |
| author_sort | Hübler, Ron |
| collection | MIT |
| 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. |
| first_indexed | 2024-09-23T14:07:32Z |
| format | Article |
| id | mit-1721.1/126318 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:07:32Z |
| publishDate | 2020 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1263182022-09-28T18:42:34Z 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 Massachusetts Institute of Technology. Institute for Medical Engineering & Science Massachusetts Institute of Technology. Department of Civil and Environmental Engineering 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. 2020-07-22T18:38:38Z 2020-07-22T18:38:38Z 2019-12-16 2019-01 2020-06-26T11:08:15Z Article http://purl.org/eprint/type/JournalArticle 1474-760X https://hdl.handle.net/1721.1/126318 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) en 10.1186/s13059-019-1903-0 Genome Biology Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s). application/pdf BioMed Central BioMed Central |
| spellingShingle | 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 |
| url | https://hdl.handle.net/1721.1/126318 |
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