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...

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Bibliographic Details
Published in:PloS one 2011-01, Vol.6 (1), p.e15925-e15925
Main Authors: Kofler, Robert, Orozco-terWengel, Pablo, De Maio, Nicola, Pandey, Ram Vinay, Nolte, Viola, Futschik, Andreas, Kosiol, Carolin, Schlötterer, Christian
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Bioinformatics
Biology
Building codes
Chromosomes
Computer Science
Cost analysis
Data Interpretation, Statistical
Data processing
Deoxyribonucleic acid
Divergence
DNA
Drosophila
Drosophila melanogaster
Evolution
Gene loci
Gene mapping
Gene sequencing
Genetic analysis
Genetic aspects
Genetic testing
Genetics, Population
Genomes
Genomics
Humans
Insects
Internet
Models, Genetic
Mutation
Ontology
Perl
Population (statistical)
Population genetics
Quality
Sequence Analysis, DNA - methods
Sequence Analysis, DNA - statistics & numerical data
Statistical analysis
Statistical analysis of data
Statistical methods
Windows (computer programs)
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0015925