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

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.

Fig. 1.

Expected versus observed values for the tests implemented in PoPoolation2 using 10 000 simulated SNPs. (A) allele frequency difference; (B) F_ST; (C) Fisher's exact test [−log 10(P-value)]; (D) CMH test [−log 10(P-value)].