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Title: | T-lex2: Genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data |
Authors: | Fiston-Lavier, Anna-Sophie; Barrón, Maite G. CSIC ORCID; Petrov, Dmitri A.; González Pérez, Josefa CSIC ORCID | Issue Date: | 27-Feb-2015 | Publisher: | Oxford University Press | Citation: | Nucleic Acids Research 43(4): e22 (2015) | Abstract: | 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 © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. | Description: | This 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 | URI: | http://hdl.handle.net/10261/115684 | DOI: | 10.1093/nar/gku1250 | Identifiers: | doi: 10.1093/nar/gku1250 e-issn: 1362-4962 issn: 0305-1048 |
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