Durvasula Arun, Hoffman Paul J, Kent Tyler V, Liu Chaochih, Kono Thomas J Y, Morrell Peter L, Ross-Ibarra Jeffrey
Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA.
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
Mol Ecol Resour. 2016 Nov;16(6):1449-1454. doi: 10.1111/1755-0998.12578. Epub 2016 Aug 29.
High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high-throughput sequencing data. angsd uses probabilistic approaches which can directly make use of genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we present angsd-wrapper, a set of wrapper scripts that provides a user-friendly interface for running angsd and visualizing results. angsd-wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression. angsd-wrapper also provides interactive graphing of angsd results to enhance data exploration. We demonstrate the usefulness of angsd-wrapper by analysing resequencing data from populations of wild and domesticated Zea. angsd-wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper.
高通量测序改变了群体遗传学、分子生态学及相关领域的诸多方面，对实验设计和数据分析均产生了影响。软件包angsd允许用户对高通量测序数据进行多项群体遗传学分析。angsd采用概率方法，可直接利用基因型似然性；因此，比较分析无需进行单核苷酸多态性（SNP）分型。这利用了所有测序数据，对于测序深度较低的样本能产生更准确的结果。在此，我们介绍angsd-wrapper，这是一组包装脚本，为运行angsd和可视化结果提供了用户友好界面。angsd-wrapper支持多种类型的分析，包括核苷酸序列多样性估计、中性检验、主成分分析、个体样本混合比例估计以及量化近期基因渗入的统计量计算。angsd-wrapper还提供angsd结果的交互式绘图，以加强数据探索。我们通过分析野生和驯化玉米群体的重测序数据，展示了angsd-wrapper的实用性。angsd-wrapper可从https://github.com/mojaveazure/angsd-wrapper免费获取。
