EUKulele：未命名的真核微生物的分类学注释
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
摘要：
微生物物种生物多样性的评估在生态学和进化生物学中至关重要（Reaka-Kudla et al. 1996），但对于环境中发现的微生物群落尤其具有挑战性（Das et al. 2006，Hillebrand et al. 2018）。除了提供海洋生物普查之外，评估海洋微生物生物多样性还可以揭示微生物如何应对环境变化（Salazar et al. 2017），澄清社区成员的生态作用（Hehemann et al. 2016），并导致生物技术发现（Das et al. 2006）。基于环境序列数据集可用数据的质量来表征分类多样性和系统发育的计算方法对于促进我们对这些生物在环境中的作用的理解是至关重要的。更紧迫的是需要全面和一致的方法来分配分类环境相关的微生物真核生物。在这里，我们提出了EUKulele，一个开源的软件工具，旨在分配分类微真核生物检测元组学样本，并补充分析方法，在其他领域通过容纳组装输出和提供具体的指标报告每个样本的分类完整性。
英文摘要：
The assessment of microbial species biodiversity is essential in ecology and evolutionary biology (Reaka-Kudla et al. 1996), but especially challenging for communities of microorganisms found in the environment (Das et al. 2006, Hillebrand et al. 2018). Beyond providing a census of organisms in the ocean, assessing marine microbial biodiversity can reveal how microbes respond to environmental change (Salazar et al. 2017), clarify the ecological roles of community members (Hehemann et al. 2016), and lead to biotechnology discoveries (Das et al. 2006). Computational approaches to characterize taxonomic diversity and phylogeny based on the quality of available data for environmental sequence datasets is fundamental for advancing our understanding of the role of these organisms in the environment. Even more pressing is the need for comprehensive and consistent methods to assign taxonomy to environmentally-relevant microbial eukaryotes. Here, we present EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.
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