Hey, I am actually very new to this and I have few genomes to analyse. I am looking through many methods, could anyone please suggest me any good method (reliable but relatively easy to use) for identifying repetitive DNA/ transposons?
If you have large sequences to analyse, you can download the RepeatMasker app and it will be able to identify the different classes of transposons and repeat elements. RepeatMasker requires a proprietary sequence database called repbase, which can be restrictive. If you want to avoid repbase/repeatmasker there are now some alternatives like DFAM. Links below.