# Calculate the percentage of the genome that is represented by some sequences

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.

• Do you want to know how much of the genome is in your sequences in a fasta file? What have you tried to do? Any perl/python/R/bash or other tools you have used or are familiar with?
– llrs
Sep 4, 2019 at 21:36
• i combined all the library then i used repeatmasker with a flag - lib combinLibrary.fasta mygenome.fasta . but its very slow now almost one week and still far to finish, im not sure if its right but im waiting the result while waiting i thought of asking for help Sep 5, 2019 at 5:46
• Great, thanks for clarifying this. I'll edit your question to include this information. You can also edit the question to add and improve the question whenever you want
– llrs
Sep 5, 2019 at 6:59
• i thought its easy task for the expert by using any kind of scripting language , my run still far from half time. any help please Sep 9, 2019 at 10:00
• Sorry I am not an expert on genome coverage. Perhaps if you link around in social networks you get more views and hopefully an answer.
– llrs
Sep 9, 2019 at 10:19