Comparison of bioinformatics workflows (Item P)

Comparison of the performance of the Kraken+Bracken workflow described in Kirstahler <i>et al</i>. 2018, with 12 metagenomic classifiers using a synthetic mock community, as described in Peabody <i>et al.</i>, 2015. <br>Examination of the MetaSimHC250 dataset containing simulated reads from 11 microorganisms with a read length of 250 bp (Peabody <i>et al</i>., 2015). The values obtained using our Kraken+Bracken workflow (see Fig. 2 in Kirstahler <i>et al</i>., 2018) are compared with the values obtained by Peabody <i>et al</i>., 2015.<br>A) The proportion of assigned reads after classification. Kraken+Bracken performance is similar to Kraken.<br>B) Calculated sensitivity for tested methods on each individual species in the synthetic mock community. Our workflow shows comparable performance to the other Kraken results.<br>C) Calculated precision for tested methods on each individual species in the synthetic mock community. Kraken-based methods show high similarities.<br>D) Bracken results for MetaSimHC250 dataset with calculated sensitivity and precision for the classification of the Kraken+Bracken workflow.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b> <b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.

本研究针对Peabody等人2015年构建的合成模拟群落（synthetic mock community），对比了Kirstahler等人2018年报道的Kraken+Bracken分析流程与12种宏基因组分类器（metagenomic classifier）的分类表现。
本次分析采用Peabody等人2015年发布的MetaSimHC250数据集，该数据集包含11种微生物的读长为250碱基对（bp）的模拟测序读段（simulated reads）。本研究将我们的Kraken+Bracken分析流程（详见Kirstahler等人2018年发表的图2）得到的分析结果，与Peabody等人2015年的报道结果进行了比对。
A) 分类后已注释读段（assigned reads）的占比。Kraken+Bracken的分类表现与Kraken相近。
B) 针对合成模拟群落中的各单株物种，各测试方法的计算灵敏度。本研究的分析流程表现与其他基于Kraken的方法相当。
C) 针对合成模拟群落中的各单株物种，各测试方法的计算精确率。基于Kraken的各类方法表现高度相似。
D) MetaSimHC250数据集的Bracken分析结果，包含Kraken+Bracken流程的分类灵敏度与精确率计算值。

<b>参考文献</b> Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H, Pamp SJ. (2018) 人眼玻璃体体液中微生物的基因组学鉴定方法. *Scientific Reports（《科学报告》）*, doi:10.1038/s41598-018-22416-4.