I have been using minimap2 for a few month now and I just found a code that follow these steps :
minimap2 [-x preset] -d target.mmi target.fa minimap2 -a [-x preset] target.mmi query.fa > output.sam
when I never saw this
.mmi index. I always went 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 ? Meaning is it only for speed up ? Will it up speed my code if I do it ? Or it is already done without specifying it ?