PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
By Robert Kofler, P. Orozco‐terWengel, N. de Maio, Ram Vinay Pandey, V. Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer. PLoS ONE, 2011
609 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/27e4b0095156673cebcd19d3d9d7dcd51e5c9075
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In Genetics
- Julian Catchen
- J. Davey
- Mark L. Blaxter
- Paul A Hohenlohe
- Bryan C. Carstens
- S. Hird
- J. McCormack
- A. Zellmer
In Molecular Biology
- Julian Catchen
- Mark L. Blaxter
- J. Davey
- Paul A Hohenlohe
- Bryan C. Carstens
- J. McCormack
- R. T. Brumfield
- Alan R. Lemmon
Citations in the corpus
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing (2011, methodology): “Some progress is being made in statistically accounting for these issues ( Box 3 ) and several packages are now available for handling data from these method”
- Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, background): “It saves money by limiting the number of barcode adaptors or library preparations needed and can be useful for marker discovery and describing some divergence statistics such as FST (Gompert et al., 2010; Kofler et al., 2011).”