使用ArrayMaker从比对的全基因组中进行简单、快速且准确的测序基因分型。
Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
作者信息
Willet Cali E, Haase Bianca, Charleston Michael A, Wade Claire M
机构信息
Faculty of Veterinary Science and School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia.
出版信息
Bioinformatics. 2015 Feb 15;31(4):599-601. doi: 10.1093/bioinformatics/btu691. Epub 2014 Oct 21.
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 at Bioinformatics online.
CONTACT
摘要
全基因组测序彻底改变了遗传学研究。测序分型如今已成为一种可行的基因分型方法，然而，所涉及的生物信息学内容对一些实验室来说即便不是令人望而却步，也会让人觉得颇具挑战性。在此，我们介绍ArrayMaker，这是一个用户友好型工具，可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以及在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这些基因型。使用该工具，仅有基本计算能力的遗传学家就能对任何所需标记列表中的样本进行基因分型，从而便于进行全基因组关联分析、精细定位、候选变异评估、数据共享以及来自多种技术的数据源的数据兼容性分析。
可用性与实施情况
ArrayMaker遵循麻省理工学院许可协议，可从https://github.com/cw2014/ArrayMaker/免费获取。该程序用Perl语言编写，在Linux操作系统上运行。
补充信息
补充数据可在《生物信息学》在线版获取。
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