PoPoolation
|
Application data |
|
| Biological application domain(s) | Population genetics |
|---|---|
| Maintained? | Maybe |
| Programming language(s) | Perl, R |
Summary: Toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals.
"Error: no local variable "counter" was set." is not a number.
Description
Currently next generation sequencing (NGS) technologies are mainly used to sequence individuals. However, the high coverage required and the resulting costs may be prohibitive for population scale studies. Sequencing pools of individuals instead may often be more cost effective and more accurate than sequencing individuals. PoPoolation is a pipeline for analysing pooled next generation sequencing data. PoPoolation builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf) or for synonymous and non-synonymous sites. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.
Limitations/Pitfalls:
Calculating the correction factors takes prohibitively long when the coverage is larger than 500. In this case uncorrected Tajima's Pi, Wattersons's Theta and Tajima's D may be computed instead.
Links
References
To add a reference for PoPoolation, enter the PubMed ID in the field below and click 'Add'.
Search for "PoPoolation" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
