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

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

Author information

1
Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.

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.

PMID:
22025480
PMCID:
PMC3232374
DOI:
10.1093/bioinformatics/btr589
[Indexed for MEDLINE]
Free PMC Article

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