How to speed up for big genome?

[zyworship]

Hi dear Shujun,
I have configured the environment for computing about the EDTA.
But I work on genome for amphibians, the genome size is bigger than other animals. I have run EDTA_raw for TIR, LTR, helitron.EDTA_raw.pl -genome frog1_genome.chromosome.fa -type tir -thrads 16. It's been running for 48 hours and it's not finished yet.
Is there any methods for speed up for big genomes?

Thank you for your attention and reply.

Zhangyi

[oushujun]

Dear @zyworship,

48 hours on a big genome is a VERY short time. You may want to give it a week or more. Think about the time for gene predictions your genome may take, EDTA is no less simple or faster at the moment. Your way of splitting the EDTA_raw.pl is the recommended way to speed up EDTA. While waiting for TIR to finish, you may also run -type ltr and -type helitron at the same time in the same folder in different jobs.

Best,
Shujun