Work

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

Year: 2011

Type: article

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: [email protected] 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btr589

Authors: Robert Kofler, Ram Vinay Pandey, Christian Schlötterer

Institution: University of Veterinary Medicine Vienna

Language: English

Topic: Genetic diversity and population structure

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,989

Funder: Austrian Science Fund