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

PLoS One. 2011 Jan 6;6(1):e15925. doi: 10.1371/journal.pone.0015925.


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 types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Data Interpretation, Statistical
  • Genetics, Population
  • Humans
  • Internet
  • Models, Genetic
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / statistics & numerical data*