I have been using minimap2 for a few month now and I just found a script that follows these steps:
minimap2 [-x preset] -d target.mmi target.fa minimap2 -a [-x preset] target.mmi query.fa > output.sam
I have never seen this
.mmi index before. I always used minimap2 directly like this:
minimap2 -a [-x preset] target.fa query.fastq > output.sam
So my question is why should I index my reference genome before mapping? Is it only for speed up? Will it up speed my code if I do it? Or it is already done without specifying it?