Introduction

Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex.

Publications

  1. T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
    Cite this
    Fiston-Lavier AS, Barrón MG, Petrov DA, González J, 2015-02-01 - Nucleic acids research
  2. T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
    Cite this
    Fiston-Lavier AS, Carrigan M, Petrov DA, González J, 2011-03-01 - Nucleic acids research

Credits

  1. Anna-Sophie Fiston-Lavier
    Developer

    Department of Biology, Stanford University, United States of America

  2. Maite G Barrón
    Developer

    Genomics, Bioinformatics and Evolution Group, Spain

  3. Dmitri A Petrov
    Developer

    Department of Biology, Stanford University, United States of America

  4. Josefa González
    Investigator

    Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain

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Summary
AccessionBT006916
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionSpain
Submitted ByJosefa González