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

Abstract

Abstract 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.

Keywords

GenotypingBiologyReference genomeGeneticsGenomeComputational biologySingle-nucleotide polymorphismWhole genome sequencingPopulationSNP genotypingGenotypeGene

Affiliated Institutions

University of Oregon US

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Publication Info

Year: 2011
Type: article
Volume: 1
Issue: 3
Pages: 171-182
Citations: 1966
Access: Closed

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APA Style

                            
                                
                                    Julian Catchen, 
                                
                                    Angel Amores, 
                                
                                    Paul A. Hohenlohe
                                
                                et al.
                            
                            (2011). 
                            <i>Stacks</i>: Building and Genotyping Loci <i>De Novo</i> From Short-Read Sequences. 
                            G3 Genes Genomes Genetics
                            , 1
                            (3)
                            , 171-182.
                            https://doi.org/10.1534/g3.111.000240
                        

Identifiers

DOI: 10.1534/g3.111.000240