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• PoPoolation TE2
• Manual
  • Selected topics
  • Walkthrough
• Cite
• Release history
• Related projects
• Authors

PoPoolation TE2

PopoolationTE2 is designed to enable an unbiased comparision of TE abundance between multiple samples, where samples could be pooled populations, tissues or sequenced individuals. PoPoolationTE2 requires paired end reads for at least one sample, a reference genome and a either set of TE consensus sequences or a TE annotation.

Manual

• [Introduction and basic concepts]
• [Manual]
• [DriverScripts] we provide driver scripts (shell scripts) for automating some of the workflows
• [ComputingTime] overview of the required computing time using real Pool-Seq data
• [FAQ]

Selected topics

• [ppileup file] introducing the physical pileup file, the major innovation implemented in PoPoolationTE2
• [signatures of TE insertions] how signatures of TE insertions are identified with PoPoolationTE2
• [signature modes] the reason why we introduced three different algorithm for identifying signatures of TE insertions
• [estimate frequency] how population frequencies of TEs are estimated in PoPoolationTE2
• [signature file format]
• [TE insertion file] the final output - a file containing TE insertions for all samples
• [diverse output files] formats of diverse secondary output files
• [TE-Benchmark] files for benchmarking tools for the identification of TE insertions from Pool-Seq data

Walkthrough

• [WalkthroughPreparatoryWork] demonstrates how the TE-merged-reference and the TE-hierarchy, two prerequisites for running PoPoolationTE2, can be created
• [Walkthrough] demonstrates the usage of PoPoolationTE2 using a small sample dataset

Cite

PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq
Robert Kofler, Daniel Gomez-Sanchez, Christian Schloetterer (in press) Molecular Biology and Evolution
http://mbe.oxfordjournals.org/content/early/2016/07/22/molbev.msw137.abstract

Release history

• [ReleaseHistory]

Related projects

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 TE: Predecessor of PoPoolationTE2; A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations

PoPoolation DB: A user-friendly web-based database for the retrieval of natural variation in Drosophila melanogaster

Authors

• Robert Kofler
• Christian Schlötterer

Project Members:

• Daniel Gómez-Sánchez
• Robert Kofler (admin)