PoPoolation: a toolbox for population genetic analysis of 2nd generation sequencing data from pooled individuals

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