Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
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使用 ArrayMaker 对比对的全基因组进行简单、快速且准确的测序基因分型。
DOI：
10.1093/bioinformatics/btu691
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
Wade,ClaireM
中科院分区：
文献类型：
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作者：
Willet,CaliE;Haase,Bianca;Charleston,MichaelA;Wade,ClaireM
摘要：全基因组测序彻底改变了遗传学研究。通过测序进行基因分型现在是一种可行的基因分型方法，但所涉及的生物信息学对于某些实验室来说即使不是令人望而却步，也可能令人望而生畏。在这里，我们介绍 ArrayMaker，这是一种用户友好的工具，可以从全基因组比对中提取预定义位点的准确单核苷酸多态性基因型，并以与关联分析软件和商业阵列平台上基因分型的数据集兼容的标准基因分型格式呈现它们。使用此工具，仅具有基本计算能力的遗传学家可以在任何所需的标记列表上对样本进行基因分型，从而促进全基因组关联分析、精细绘图、候选变异评估、数据共享和来自多种技术的数据的兼容性。可用性和实施：ArrayMaker 已获得 MIT 许可，可以在 https://github.com/cw2014/ArrayMaker/ 上免费获得。该程序用 Perl 实现，并在 Linux 操作系统上运行。补充信息：补充数据可在 Bioinformaticsonline 获取。联系方式：cali.willet@sydney.edu.au
Summary:Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies.Availability and implementation:ArrayMaker is licensed under The MIT License and can be freely obtained at https://github.com/cw2014/ArrayMaker/. The program is implemented in Perl and runs on Linux operating systems.Supplementary information:Supplementary Data are available atBioinformaticsonline.Contact:cali.willet@sydney.edu.au