What is the best way to map/align my reads on a given genome?
This is a pretty straightforward analysis, assuming that you want to measure something like &quot;how many reads align to genome 1, and how many reads align to genome 2?&quot;.

The bowtie2 manual has a section on this.
There are other tutorials for bowtie2.
bwa is also well-suited to this task.

You should be able to then use samtools to compute statistics on your alignments.