panREPET is described in this preprint available on BioRxiv

Project information

panREPET is a pipeline detecting shared Transposable Element (TE) insertions among a pangenome. It takes in charge multiple de novo whole-genome assemblies of the same species. It compares TE copies between each pair of genomes then identifies TE copies shared by a group of individuals.

Code available here :  https://forgemia.inra.fr/urgi-anagen/panREPET

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