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Title

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

AuthorsFiston-Lavier, Anna-Sophie; Barrón, Maite G. ; Petrov, Dmitri A.; González Pérez, Josefa
Issue Date27-Feb-2015
PublisherOxford University Press
CitationNucleic Acids Research 43(4): e22 (2015)
AbstractTransposable 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 © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
DescriptionThis is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Publisher version (URL)http://dx.doi.org/10.1093/nar/gku1250
URIhttp://hdl.handle.net/10261/115684
DOIhttp://dx.doi.org/10.1093/nar/gku1250
Identifiersdoi: 10.1093/nar/gku1250
e-issn: 1362-4962
issn: 0305-1048
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