J. Daron and R. K. Slotkin, EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels, Genome Biology, vol.18, issue.1, p.91, 2017.

D. S. Day, L. J. Luquette, P. J. Park, and P. V. Kharchenko, Estimating enrichment of repetitive elements from high-throughput sequence data, Genome biology, vol.11, p.69, 2010.

J. D. Debarry, R. Liu, and J. L. Bennetzen, Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm, BMC Bioinformatics, vol.9, p.235, 2008.

E. Debladis, C. Llauro, M. C. Carpentier, M. Mirouze, and O. Panaud, Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology, BMC Genomics, vol.18, issue.1, p.537, 2017.
URL : https://hal.archives-ouvertes.fr/ird-01626046

O. Delgrange and E. Rivals, STAR: an algorithm to Search for Tandem Approximate Repeats, Bioinformatics, vol.20, pp.2812-2820, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00108544

E. Disdero and J. Filée, LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences, Mobile DNA, vol.8, p.5, 2017.

A. P. Dowsett and M. W. Young, Differing levels of dispersed repetitive DNA among closely related species of Drosophila., Proceedings of the National Academy of Sciences, vol.79, issue.15, pp.4570-4574, 1982.

G. Dumbovic, N. V. Forcales, and M. Perucho, Emerging roles of macrosatellite repeats in genome organization and disease development, Epigenetics, vol.12, issue.7, pp.515-526, 2017.

R. C. Edgar and E. W. Myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, pp.i152-i158, 2005.

S. R. Eichten, N. A. Ellis, I. Makarevitch, C. Yeh, J. I. Gent et al., Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons, PLoS Genetics, vol.8, issue.12, p.e1003127, 2012.

D. Ellinghaus, S. Kurtz, and U. Willhoeft, LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, vol.9, issue.1, p.18, 2008.

T. A. Elliott and T. R. Gregory, What's in a genome? The C-value enigma and the evolution of eukaryotic genome content, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.370, issue.1678, p.20140331, 2015.

M. R. Estécio, J. Gallegos, and M. Dekmezian, SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters, Molecular Cancer Research, vol.10, pp.1332-1342, 2012.

A. D. Ewing, Transposable element detection from whole genome sequence data, Mobile DNA, vol.6, p.24, 2015.

C. Feschotte, U. Keswani, N. Ranganathan, M. L. Guibotsy, and D. Levine, Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes, Genome Biology and Evolution, vol.1, pp.205-220, 2010.

A. S. Fiston-lavier, M. G. Barrón, D. A. Petrov, and J. González, T-lex2: Genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data, Nucleic Acids Research, vol.43, p.22, 2015.

T. Flutre, E. Duprat, C. Feuillet, and H. (. Quesneville, Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.6, issue.1, p.e16526, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00568705

E. J. Gardner, V. K. Lam, and D. N. Harris, The Mobile Element Locator Tool (MELT): Population-scale mobile element discovery and biology, Genome Research, 2017.

R. Ge, G. Mai, and R. Zhang, MUSTv2: An improved de novo detection program for recently active Miniature Inverted repeat Transposable Elements (MITEs), Journal of Integrative Bioinformatics, p.14, 2017.

Y. Gelfand, Y. Hernandez, and J. Loving, VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data, Nucleic Acids Research, vol.42, pp.8884-8894, 2014.

A. Gilly, M. Etcheverry, and M. A. Madoui, De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti), Genome Biology and Evolution, vol.15, pp.1192-1205, 2014.

M. G. Grabherr, B. J. Haas, and M. Yassour, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature biotechnology, vol.29, pp.644-652, 2011.

B. W. Han, W. Wang, P. D. Zamore, and Z. Weng, piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome-and CAGE-seq, ChIP-seq and genomic DNA sequencing, Bioinformatics, vol.31, pp.593-595, 2015.

Y. Han and S. R. Wessler, MITE-Hunter: A program for discovering miniature inverted-repeat transposable elements from genomic sequences, Nucleic Acids Research, vol.38, pp.1-8, 2010.

D. C. Hancks and H. H. Kazazian, Active human retrotransposons: Variation and disease. Current Opinion in Genetics and Development, vol.22, pp.191-203, 2012.

E. Helman, M. S. Lawrence, and C. Stewart, Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing, Genome Research, vol.24, pp.1053-1063, 2014.

E. Hénaff, L. Zapata, J. M. Casacuberta, and S. Ossowski, Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution, BMC Genomics, vol.16, p.768, 2015.

C. Hoede, S. Arnoux, and M. Moisset, PASTEC: an automatic transposable element classification tool, PLoS ONE, vol.9, p.91929, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639360

D. R. Hoen, G. Hickey, and G. Bourque, A call for benchmarking transposable element annotation methods, Mobile DNA, vol.6, p.13, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01204840

C. Jiang, C. Chen, Z. Huang, R. Liu, and J. Verdier, ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data, BMC Bioinformatics, p.72, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01605647

V. Kapitonov and J. Jurka, A universal classification of eukaryotic transposable elements implemented in Repbase, Nature reviews Genetics, vol.9, pp.411-412, 2008.

T. M. Keane, K. Wong, and D. J. Adams, RetroSeq: Transposable element discovery from nextgeneration sequencing data, Bioinformatics, vol.29, pp.389-390, 2013.

M. G. Kidwell and D. R. Lisch, Transposable elements and host genome evolution, Trends in Ecology & Evolution, vol.15, issue.3, pp.95-99, 2000.

B. Mcclintock, The origin and behavior of mutable loci in maize, Proceedings of the National Academy of Sciences of the United States of America, vol.36, pp.344-355, 1950.

R. C. Mccoy, R. W. Taylor, and T. A. Blauwkamp, Illumina TruSeq Synthetic Long-Reads empower de novo assembly and resolve complex, highly-repetitive transposable elements, PLoS ONE, vol.9, p.106689, 2014.

Y. Miki, I. Nishisho, and A. Horii, Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer, Cancer Research, vol.52, pp.643-645, 1992.

L. Modolo and E. Lerat, Identification and analysis of transposable elements in genomic sequences, pp.165-181, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02099541

A. M. Newman and J. B. Cooper, XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences, BMC Bioinformatics, vol.8, p.382, 2007.

P. Novák, P. Neumann, J. Pech, J. Steinhais, and J. Macas, RepeatExplorer: A Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from nextgeneration sequence reads, Bioinformatics, vol.29, pp.792-793, 2013.

P. Novák, L. Ávila-robledillo, and A. Koblí?ková, TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads, Nucleic acids research, vol.45, p.111, 2017.

P. Novák, P. Neumann, and J. Macas, Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data, BMC Bioinformatics, vol.11, issue.1, p.378, 2010.

M. Pendleton, R. Sebra, A. W. Pang, A. Ummat, O. Franzen et al., Assembly and diploid architecture of an individual human genome via single-molecule technologies, Nature Methods, vol.12, issue.8, pp.780-786, 2015.

D. A. Petrov, A. S. Fiston-lavier, M. Lipatov, K. Lenkov, and J. Gonzalez, Population Genomics of Transposable Elements in Drosophila melanogaster, Molecular Biology and Evolution, vol.28, issue.5, pp.1633-1644, 2010.

R. N. Platt, L. Blanco-berdugo, and D. A. Ray, Accurate transposable element annotation is vital when analyzing new genome assemblies, Genome Biology and Evolution, vol.8, pp.403-410, 2016.

A. Platzer, V. Nizhynska, and Q. Long, TE-Locate: A tool to locate and group transposable element occurrences using paired-end next-generation sequencing data, Biology, vol.1, pp.395-410, 2012.

A. L. Price, N. C. Jones, and A. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics, vol.21, pp.351-358, 2005.

R. Rahman, G. W. Chirn, and A. Kanodia, Unique transposon landscapes are pervasive across Drosophila melanogaster genomes, Nucleic acids research, vol.43, pp.10655-10672, 2015.

M. Rho, J. H. Choi, S. Kim, M. Lynch, and H. Tang, De novo identification of LTR retrotransposons in eukaryotic genomes, BMC genomics, vol.8, p.90, 2007.

G. Richard, A. Kerrest, and B. Dujon, Comparative genomics and molecular dynamics of DNA repeats in eukaryotes, Microbiology and molecular biology reviews, vol.72, pp.686-727, 2008.

L. Rishishwar, L. Mariño-ramírez, and I. K. Jordan, Benchmarking computational tools for polymorphic transposable element detection, Briefings in Bioinformatics, p.72, 2016.

S. M. Robb, L. Lu, and E. Valencia, The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice, vol.3, pp.949-957, 2013.

W. G. Rostant, N. Wedell, and D. J. Hosken, Transposable elements and insecticide resistance, Advances in genetics, vol.78, pp.169-201, 2012.

S. Saha, S. Bridges, Z. V. Magbanua, and D. G. Peterson, Computational approaches and tools used in identification of dispersed repetitive DNA sequences, Tropical Plant Biology, vol.1, pp.85-96, 2008.

N. Santiago, C. Herráiz, J. R. Goñi, X. Messeguer, and J. M. Casacuberta, Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana, Molecular biology and evolution, vol.19, pp.2285-2293, 2002.

S. Schnable, D. Ware, and R. S. Fulton, The B73 maize genome: complexity, diversity, and dynamics, Science, vol.326, pp.1112-1115, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00751527

Y. Segal, B. Peissel, and A. Renieri, LINE-1 elements at the sites of molecular rearrangements in Alport syndrome-diffuse leiomyomatosis, American journal of human genetics, vol.64, pp.62-69, 1999.

A. J. Sharp, D. P. Locke, S. D. Mcgrath, Z. Cheng, J. A. Bailey et al., Segmental Duplications and Copy-Number Variation in the Human Genome, The American Journal of Human Genetics, vol.77, issue.1, pp.78-88, 2005.

D. Sokol, G. Benson, and J. Tojeira, Tandem repeats over the edit distance, Bioinformatics, vol.23, issue.2, pp.e30-e35, 2007.

S. E. Staton and J. M. Burke, Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads, Bioinformatics, vol.31, issue.11, pp.1827-1829, 2015.

S. Steinbiss, U. Willhoeft, G. Gremme, and S. Kurtz, Fine-grained annotation and classification of de novo predicted LTR retrotransposons, Nucleic Acids Research, vol.37, issue.21, pp.7002-7013, 2009.

S. T. Szak, O. K. Pickeral, and W. Makalowski, Molecular archeology of L1 insertions in the human genome, Genome biology, vol.3, p.52, 2002.

D. T. Thung, J. De-ligt, and L. E. Vissers, Mobster: accurate detection of mobile element insertions in next generation sequencing data, Genome Biology, vol.15, p.488, 2014.

T. J. Treangen and S. L. Salzberg, Repetitive DNA and next-generation sequencing: computational challenges and solutions, Nature Reviews Genetics, vol.13, issue.1, pp.36-46, 2011.

Z. Tu, S. Li, and C. Mao, The Changing Tails of a Novel Short Interspersed Element inAedes aegypti, Genetics, vol.168, issue.4, pp.2037-2047, 2004.

J. M. Tubio, Y. Li, and Y. S. Ju, L1 Retrotransposition Transduces Nonrepetitive DNA throughout Cancer Genomes, Cancer Discovery, vol.4, issue.10, pp.1115-1115, 2014.

R. H. Waterston, K. Lindblad-toh, and E. Birney, Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-62, 2002.

T. Wicker, E. Schlagenhauf, A. Graner, T. J. Close, B. Keller et al., 454 sequencing put to the test using the complex genome of barley, BMC Genomics, vol.7, issue.1, p.275, 2006.

T. Wicker, F. Sabot, and A. Hua-van, A unified classification system for eukaryotic transposable elements, Nature reviews Genetics, vol.8, pp.973-982, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00169819

J. Wu, W. P. Lee, A. Ward, J. A. Walker, M. K. Konkel et al., Tangram: a comprehensive toolbox for mobile element insertion detection, BMC Genomics, vol.15, issue.1, p.795, 2014.

Z. Xu and H. Wang, LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Research, vol.35, issue.Web Server, pp.W265-W268, 2007.

J. Zhuang, J. Wang, W. Theurkauf, and Z. Weng, TEMP: a computational method for analyzing transposable element polymorphism in populations, Nucleic Acids Research, vol.42, issue.11, pp.6826-6838, 2014.

M. Zytnicki, E. Akhunov, and H. Quesneville, Tedna: a transposable element de novo assembler, Bioinformatics, vol.30, issue.18, pp.2656-2658, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02630617