articleBioinformaticsOct 23, 2011HYBRID OA

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

RKRobert KoflerRVRam Vinay PandeyCSChristian Schlötterer

University of Veterinary Medicine Vienna

PubMed
Indexed incrossrefdoajpubmed

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:…

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911
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Authors

3

Topics & keywords

Topics
Keywords
  • Perl
  • DNA sequencing
  • Computer science
  • Software
  • Code (set theory)
  • Population
  • Genomics
  • Biology
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