PoPoolation2: Identifying Differentiation Between Populations Using Sequencing of Pooled DNA Samples (Pool-Seq)

Bioinformatics. 2011 Dec 15;27(24):3435-6. doi: 10.1093/bioinformatics/btr589. Epub 2011 Oct 23.

Abstract

Summary: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer.

Availability and implementation: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/

Contact: christian.schloetterer@vetmeduni.ac.at

Supplementary information: Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis / genetics
  • Drosophila melanogaster / genetics
  • Genetics, Population / methods*
  • Genomics
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • Software*