Stacks: building and genotyping Loci de novo from short-read sequences.
Stacks: building and genotyping Loci de novo from short-read sequences.
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DOI：
10.1534/g3.111.000240
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发表时间：
2011-08
期刊：
影响因子：
--
通讯作者：
Postlethwait JH
中科院分区：
文献类型：
--
作者：
Catchen JM;Amores A;Hohenlohe P;Cresko W;Postlethwait JH
测序技术的进步为快速和节俭地对个体进行基因分型提供了特殊的机会，但缺乏软件来自动调用数百个个体的数万种基因型，这阻碍了进展。Stacks是一种软件系统，其使用短读段序列数据来重新鉴定或通过与参考基因组比较来鉴定一组个体中的基因座并对其进行基因分型。从简化的Illumina序列数据，如RAD标签，Stacks可以恢复数千个单核苷酸多态性（SNP）标记，用于杂交或种群的遗传分析。堆栈可以产生标记的超密集遗传连锁图谱，促进人口地理学的检查，并帮助参考基因组组装。我们在这里报告的算法实现堆栈和证明其有效性，从模拟的RAD标签从刺鱼参考基因组构建位点，并通过重述和改进的斑马鱼，斑马鱼的遗传图谱。
Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. We report here the algorithms implemented in Stacks and demonstrate their efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio.
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影响因子：
4.4
作者：
Koop, Ben F.;von Schalburg, Kristian R.;Leong, Jong;Walker, Neil;Lieph, Ryan;Cooper, Glenn A.;Robb, Adrienne;Beetz-Sargent, Marianne;Holt, Robert A.;Moore, Richard;Brahmbhatt, Sonal;Rosner, Jamie;Rexroad, Caird E., III;McGowan, Colin R.;Davidson, William S.
通讯作者：
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影响因子：
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通讯作者：
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7
作者：
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影响因子：
7.7
作者：
Hohenlohe, Paul A.;Amish, Stephen J.;Luikart, Gordon
通讯作者：
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影响因子：
1.7
作者：
Phillips, R. B.;Amores, A.;Postlethwait, J. H.
通讯作者：
Postlethwait, J. H.