popoolationte Wiki
Brought to you by:
rokofler
Menu
▾
▴
Main
Introduction
PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing. PoPoolation TE calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions.
PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).
Note the successor PoPoolationTE2 is available here
How to cite PoPoolation TE
- Robert Kofler, Andrea Betancourt and Christian Schloetterer (2012): Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster; PLoS Genetics http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002487
You may also be interested in our Pool-seq review (Nature Reviews Genetics) where we provide some recommendations for the analysis of Pool-seq data:
Usage
Related projects
PoPoolation TE2 A tool for comparing the transposable element (TE) abundance between sample, where samples could be pooled populations, tissues or sequenced individuals. It identifies novel as well as known TE insertions and reports the population frequencies of all TEs in all samples.
Gowinda: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:
PoPoolation: A pipeline for analyzing pooled next generation sequencing data for single populations. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D for reference sequences using a sliding window approach
PoPoolation2: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
PoPoolation DB: A user-friendly web-based database for the retrieval of natural variation in Drosophila melanogaster
