Finding transposable elements using RepeatMasker
You need to model the repeats in your de novo genome.

See:
http://www.repeatmasker.org/RepeatModeler/ and
https://www.biostars.org/p/154290/ (from previous answer)

You first build a database named "name_of_your_database" (insert whatever you want to call it) and run it on the fasta file of your genome (e.g. your_genome.fasta).

Make you find the right paths for the software.

## build the database
BuildDatabase -engine ncbi -name name_of_your_database your_genome.fasta

## run the modeler (in this case using ncbi)
RepeatModeler -database name_of_your_database -engine ncbi