Hello! I'm searching for suggestion about the new best pipeline/s to find TRANSPOSABLE ELEMENTS in a new assembled genome of a no reference species (octopus). I don't want to use repeatmasker.
Can anyone help me?
RepeatMasker is a viable solution if you already have a database of TEs from a very close specie.
With RepeatMasker and Repbase, you won't be able to detect all mobile elements specific to your newly assembled genome. Moreover, your annotation will be polluted by false positive.
REPET perform de novo detection by only using the genome sequence. It's quite heavy computation, but if your genome is too big or too repeated, you could apply an iterative strategy to reduce complexity. This way you will find the specific population of TE for your genome and do an exhaustive annotation of all the copies even for the very oldest ones.