I have construct a repeat libraries using de-novo identification methods. All results from different tools has been combined into one fasta file.
How can I get the percentage of how much these sequences are found in the original genome? That has been used earlier for repeat detections.
For example these identified candidates account for 30% from the total genome.
I used repeatmasker with a flag
-lib combinLibrary.fasta mygenome.fasta but its very slow now almost one week and still far to finish.