Introduction

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

Publications

  1. Stacks: an analysis tool set for population genomics.
    Cite this
    Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA, 2013-06-01 - Molecular ecology
  2. Stacks: building and genotyping Loci de novo from short-read sequences.
    Cite this
    Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH, 2011-08-01 - G3 (Bethesda, Md.)

Credits

  1. Julian Catchen
    Developer

    Institute of Ecology and Evolution, University of Oregon, United States of America

  2. Paul A Hohenlohe
    Developer

  3. Susan Bassham
    Developer

  4. Angel Amores
    Developer

  5. William A Cresko
    Investigator

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Summary
AccessionBT003240
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByWilliam A Cresko