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T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Anna-Sophie Fiston-Lavier, Maite G. Barrón, Dmitri A. Petrov, Josefa González
doi: https://doi.org/10.1101/002964
Anna-Sophie Fiston-Lavier
1Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
2Institut des Sciences de l’Evolution (ISEM), UMR5554 CNRS-Université Montpellier 2, France
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Maite G. Barrón
3Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina-IBB/Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
4Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain.
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Dmitri A. Petrov
1Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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Josefa González
4Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain.
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ABSTRACT

Transposable elements (TEs) are the most active, diverse and ancient component in a broad range of genomes. As such, a complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analyses of TEs still represent 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 (NGS) 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. Although we tested the fidelity of T-lex2 using the high quality Drosophila melanogaster genome, the flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. 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://petrov.stanford.edu/cgi-bin/Tlex.html.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 24, 2014.
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T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
Anna-Sophie Fiston-Lavier, Maite G. Barrón, Dmitri A. Petrov, Josefa González
bioRxiv 002964; doi: https://doi.org/10.1101/002964
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T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
Anna-Sophie Fiston-Lavier, Maite G. Barrón, Dmitri A. Petrov, Josefa González
bioRxiv 002964; doi: https://doi.org/10.1101/002964

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