title: T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
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.
authors.affiliation: Department of Biology, Stanford University, Stanford, CA 94305-5020, USA Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR5554 CNRS-Université Montpellier 2, France asfiston@univ-montp2.fr.
authors.forename: Anna-Sophie
authors.initials: AS
authors.lastname: Fiston-Lavier
authors.affiliation: Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina - IBB/Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.
authors.forename: Maite G
authors.initials: MG
authors.lastname: Barrón
authors.affiliation: Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Petrov
authors.affiliation: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.
authors.forename: Josefa
authors.initials: J
authors.lastname: González
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D015894:Genome, Human; D049750:Genome, Insect; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020071:Interspersed Repetitive Sequences; D058977:Molecular Sequence Annotation / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software