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

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 ?(Watterson), ?(?), 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.

SUBMITTER: Kofler R 

PROVIDER: S-EPMC3017084 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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

Kofler Robert R   Orozco-terWengel Pablo P   De Maio Nicola N   Pandey Ram Vinay RV   Nolte Viola V   Futschik Andreas A   Kosiol Carolin C   Schlötterer Christian C  

PloS one 20110106 1

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  ...[more]

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