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

Kayser, Manfred, Kofler, Robert, Orozco-terWengel, Pablo, De Maio, Nicola, Pandey, Ram Vinay, Nolte, Viola, Futschik, Andreas, Kosiol, Carolin and Schlötterer, Christian 2011. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE 6 (1) , e15925. 10.1371/journal.pone.0015925

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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 θWatterson, θπ, 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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Publisher: Public Library of Science
ISSN: 1932-6203
Last Modified: 04 Jun 2017 06:39
URI: http://orca.cf.ac.uk/id/eprint/63267

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