Ecology, Conservation, and Environment Center, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Sci China Life Sci. 2013 Jan;56(1):73-81. doi: 10.1007/s11427-012-4423-7. Epub 2012 Dec 27.
A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.
许多生态学和环境管理中的基础和应用问题都需要对土壤和凋落物动物区系多样性进行特征描述。高通量测序技术在条码基因扩增子（“宏条形码”）方面的最新进展使得以一种稳健而高效的方式调查生物多样性成为可能。然而，这项技术广泛采用的一个障碍是需要在许多候选生物信息学处理原始测序数据的方法中进行选择。我们比较了三种用于处理来自固体基质的 18S 小亚基 rDNA 宏条形码数据的候选管道：（i）USEARCH/CROP，（ii）Denoiser/UCLUST，和（iii）OCTUPUS。这三个管道产生了令人放心的相似且高度相关的群落组成评估，这些评估主要由已知能够描述采样环境的类群主导。然而，由于序列噪声较高，OCTUPUS 似乎会夸大系统发育多样性。因此，我们建议使用 USEARCH/CROP 或 Denoiser/UCLUST 这两个管道，它们都可以在 QIIME（微生物生态学的定量分析）环境中运行。
