However, short-read sequencing data are not suitable for the optimal detection of structural variations (SV), especially SV due to TE insertion/deletion. They rely on three main mapping features: split reads, unpaired reads, and depth of coverage. Therefore, many tools have been developed to use short-read sequencing data to identify potential TE polymorphisms among samples (e.g., T-lex McClintock ) or within a population (e.g., DNApipeTE PoPoolationTE2 ). One of the main findings provided by the availability of massive sequencing data is that TEs are the most variable component of genomes, even more than previously suspected. Nowadays, it is not uncommon to sequence the same population many times over generations to study its genetic evolution. Sequencing technology advances in the last 15 years, especially Illumina short-read sequencing, have allowed sequencing, on a daily basis, not only individuals within a species or subspecies, but also within whole populations. Moreover, tracking the presence or absence of a given insertion among individuals or through generations was, up to recently, limited to heavy wet-laboratory approaches, with a low throughput. , REPET, RepeatMasker, EDTA ), with more or less success, and requiring all a large amount of computational resources. Many tools have been developed to tackle this issue (e.g. Indeed, identifying insertions in a newly assembled genome is a hard and complex task. However, their identification, annotation, and dynamic tracking are complex due to their intrinsic repetitive nature. For instance, the Drosophila melanogaster genome is only 180Mb long, but almost ~15% of it is made of TEs. In large genomes, they represent more than 90% of nuclear DNA, but they whatever are a major component of smaller genomes. Their size ranges from less than 100 bp (e.g., for MITEs ) to more than 20kb. They are present in almost all genomes that have been analyzed and are represented by various structures and mobility mechanisms. Transposable elements (TEs) are endogenous mobile elements that can move within their host genome and increase their copy number, autonomously or not.
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