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

Catchen, Julian; Amores, Angel; Hohenlohe, Paul A.; Cresko, William A.; Postlethwait, John H.

doi:10.1534/g3.111.000240

articleG3 Genes Genomes GeneticsAug 1, 2011GOLD OA

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

JCJulian Catchen AAAngel Amores PAPaul A. Hohenlohe WAWilliam A. Cresko JHJohn H. Postlethwait

University of Oregon

PubMed

Indexed incrossrefdoajpubmed

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…

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Topics & keywords

Topics

Keywords

Genotyping
Biology
Reference genome
Genetics
Genome
Computational biology
Single-nucleotide polymorphism
Whole genome sequencing

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