Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences

G3: Genes, Genomes, Genetics

Paul Hohenlohe¹  William Cresko¹  John H. Postlethwait²  Angel Amores²  Julian M. Catchen¹ 

[1] Center for Ecology and Evolutionary BiologyCenter for Ecology and Evolutionary BiologyCenter for Ecology and Evolutionary Biology;Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403

关键词: Illumina;    meiotic linkage map;    RAD-seq;    RAD-tag;    zebrafish;   

DOI  :  10.1534/g3.111.000240

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

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.

【 授权许可】

Unknown