# Why indexing sequence file with minimap2?

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 ?

• It's a suggestion for reducing the mapping time. It's the same approach like others mappers e.g. BWA, Bowtie2, etc. Mar 4 '20 at 14:49