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Summary: Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events.For complete details on the use and execution of this protocol, please refer to Pascarella et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.