HOPS: automated detection and authentication of pathogen DNA in archaeological remains
HOPS: automated detection and authentication of pathogen DNA in archaeological remains
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DOI：
10.1186/s13059-019-1903-0
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发表时间：
2019-12-16
期刊：
影响因子：
12.3
通讯作者：
Herbig, Alexander
中科院分区：
文献类型：
--
作者：
Huebler, Ron;Key, Felix M.;Herbig, Alexander
高通量DNA测序使复杂生物系统的大规模元基因组分析成为可能。这种分析并不局限于今天的样本，也可以应用于考古遗迹的分子数据。对古代微生物的研究可以提供关于过去细菌共生和病原体的有价值的信息，但它们的分子检测仍然是一个挑战。在这里，我们介绍了HOPS(病原体筛选的启发式操作)，这是一种针对古代DNA序列的自动化细菌筛选管道，提供了关于物种鉴定和真实性的详细信息。啤酒花是一种从考古材料中高通量筛选DNA的通用工具，以确定基因组水平分析的候选对象。
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.