SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?
SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?
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DOI：
10.1186/s12864-017-3501-4
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发表时间：
2017-03-14
期刊：
影响因子：
4.4
通讯作者：
Huson DH
中科院分区：
文献类型：
--
作者：
Balvočiūtė M;Huson DH
微生物组测序分析的关键步骤是对分类单位的读段分配。这通常使用四种分类学分类之一进行，即SILVA，RDP，Greengenes或NCBI。目前还不清楚这些数据有多相似，以及如何比较基于不同分类法的分析结果。我们提供了一种方法和软件，用于将分类实体从一个分类映射到另一个分类。我们用它来比较这四个分类法和开放生命树分类法（OTT）。虽然我们发现SILVA，RDP和Greengenes很好地映射到NCBI，并且所有四个都很好地映射到OTT，但将两个较大的分类映射到较小的分类是有问题的。本文的在线版本（doi：10.1186/s12864-017-3501-4）包含补充材料，可供授权用户使用。
A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies. We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT). While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic. The online version of this article (doi:10.1186/s12864-017-3501-4) contains supplementary material, which is available to authorized users.