What is a pairwise alignment sequencing? Work on your terms knowledge

Probably you want to benchmark the software that you are going to write. For that you will at first probably run simulation (generating reads from reference genome). So that you know where your reads originally came from. Now is the question which genome (ploidy level, complexity - repeats) and which technology (Illumina, 454, Ion Torrent, PacBio, Solid, ON, so on).

I don't know how much understanding you have, but if you want to write a pairwise aligner, it won't work like standard BWA. It should target shorter reference sequences (not whole genome, but let's say a list of gene sequences). It's actually underappreciated part of alignment software, which can be pretty useful for that design.