Costea Paul Igor, Munch Robin, Coelho Luis Pedro, Paoli Lucas, Sunagawa Shinichi, Bork Peer
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
PLoS One. 2017 Jul 28;12(7):e0182392. doi: 10.1371/journal.pone.0182392. eCollection 2017.
We present metaSNV, a tool for single nucleotide variant (SNV) analysis in metagenomic samples, capable of comparing populations of thousands of bacterial and archaeal species. The tool uses as input nucleotide sequence alignments to reference genomes in standard SAM/BAM format, performs SNV calling for individual samples and across the whole data set, and generates various statistics for individual species including allele frequencies and nucleotide diversity per sample as well as distances and fixation indices across samples. Using published data from 676 metagenomic samples of different sites in the oral cavity, we show that the results of metaSNV are comparable to those of MIDAS, an alternative implementation for metagenomic SNV analysis, while data processing is faster and has a smaller storage footprint. Moreover, we implement a set of distance measures that allow the comparison of genomic variation across metagenomic samples and delineate sample-specific variants to enable the tracking of specific strain populations over time. The implementation of metaSNV is available at: http://metasnv.embl.de/.
我们展示了metaSNV，这是一种用于宏基因组样本中单核苷酸变异（SNV）分析的工具，能够比较数千种细菌和古菌物种的群体。该工具使用标准SAM/BAM格式的参考基因组核苷酸序列比对作为输入，对单个样本以及整个数据集进行SNV调用，并为各个物种生成各种统计数据，包括每个样本的等位基因频率和核苷酸多样性，以及样本间的距离和固定指数。使用来自口腔不同部位的676个宏基因组样本的已发表数据，我们表明metaSNV的结果与宏基因组SNV分析的另一种实现方式MIDAS的结果相当，同时数据处理速度更快且存储占用空间更小。此外，我们实施了一组距离度量，可用于比较宏基因组样本间的基因组变异，并划定样本特异性变异，以便随时间追踪特定菌株群体。metaSNV的实现可在以下网址获取：http://metasnv.embl.de/ 。
