PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
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.
Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
Robert
R
Kofler
Pablo
P
Orozco-terWengel
Nicola
N
De Maio
Ram Vinay
RV
Pandey
Viola
V
Nolte
Andreas
A
Futschik
Carolin
C
Kosiol
Christian
C
Schlötterer
D000465:Algorithms; D001483:Base Sequence; D003627:Data Interpretation, Statistical; D005828:Genetics, Population; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data*
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