Transposable Element annotation using Next-Generation Sequencing data
The T-lex package contains two pipelines. The T-lex pipeline calls presence/absence of known TE insertions using re-sequencing data. On top of the genotyping, this pipeline also allows to re-annotate TEs and discover traces of transposition events called Target Site Duplication (TSD).
The other T-lex pipeline discovers and annotates de novo TE insertions.
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