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PLoS One. 2011 Jan 6;6(1):e15925. doi: 10.1371/journal.pone.0015925.

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.

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  • 1Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.

Abstract

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θ(Watterson), θ(π), and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.

PMID:
21253599
[PubMed - indexed for MEDLINE]
PMCID:
PMC3017084
Free PMC Article

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