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- Title
PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
- Authors
Kofler, Robert; Orozco-terWengel, Pablo; De Maio, Nicola; Pandey, Ram Vinay; Nolte, Viola; Futschik, Andreas; Kosiol, Carolin; Schlötterer, Christian
- 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.
- Publication
PloS one, 2011, Vol 6, Issue 1, pe15925
- ISSN
1932-6203
- Publication type
Journal Article
- DOI
10.1371/journal.pone.0015925