CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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DOI：
10.1101/gr.186072.114
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发表时间：
2015-07
期刊：
影响因子：
7
通讯作者：
Tyson GW
中科院分区：
文献类型：
--
作者：
Parks DH;Imelfort M;Skennerton CT;Hugenholtz P;Tyson GW
由于计算方法的进步和测序成本的大幅降低，从分离株、单细胞和宏基因组数据中大规模恢复基因组成为可能。尽管基因组草案的广度不断增加，为微生物生命的进化和功能多样性提供了关键信息，但完成所有可用的参考基因组已变得不切实际。从基因组草案中做出可靠的生物学推断需要准确估计其完整性和污染程度。目前用于评估基因组质量的方法是特设的，并且通常利用在所有细菌或古细菌基因组中保守的有限数量的“标记”基因。在这里，我们介绍CheckM，一个自动化的方法，用于评估基因组的质量，使用更广泛的一组标记基因的特定的参考基因组树内的基因组的位置和信息的搭配这些基因。我们使用合成数据和广泛的分离物、单细胞和宏基因组衍生的基因组证明了CheckM的有效性。CheckM被证明可以提供基因组完整性和污染的准确估计，并优于现有的方法。使用CheckM，我们确定了目前影响公开可用的分离物基因组的各种错误，并证明从单细胞和宏基因组数据获得的基因组在质量上差异很大。为了便于使用基因组草案，我们提出了一个客观的衡量基因组质量，可用于选择适合于特定的基因和基因组为中心的微生物群落分析的基因组。
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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