具有高多样性和虚假单例的物种丰富度估计
Species richness estimation with high diversity but spurious singletons
摘要：
在高通量测序的生态样品中存在不常见的类群，对微生物生态学家，生物信息学家和统计学家提出了挑战。很少能确定这些分类群是否真的存在于样品中或测序错误的结果。不幸的是，α多样性量化依赖于精确的频率计数，这很少能得到保证。我们提出了一个物种丰富度估计工具，预测未观察到的类群的数量和真正的单例的数量的基础上的非单例频率计数。这种方法可以被视为推理（正式估计丰富度）或探索（用于评估丰富度估计对单例计数的鲁棒性）。如果被称为breakaway_nof1的估计值与其他丰富度估计值相当，则这提供了丰富度估计值对质量控制水平（例如，嵌合体检查）。函数breakaway_nof1可以通过R包breakaway从CRAN免费获得。
英文摘要：
The presence of uncommon taxa in high-throughput sequenced ecological samples pose challenges to the microbial ecologist, bioinformatician and statistician. It is rarely certain whether these taxa are truly present in the sample or the result of sequencing errors. Unfortunately, alpha-diversity quantification relies on accurate frequency counts, which can rarely be guaranteed. We present a species richness estimation tool which predicts both the number of unobserved taxa and the number of true singletons based on the non-singleton frequency counts. This method can be treated as either inferential (for formally estimating richness) or exploratory (for assessing robustness of the richness estimate to the singleton count). If the estimate, called breakaway_nof1, is comparable to other richness estimators, this provides evidence that the richness estimate is robust to the level of quality control (eg. chimera-checking) employed in pre-processing. The function breakaway_nof1 is freely available from CRAN via the R package breakaway.
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