I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I want to use a tool that is aware of the annotation of exon and intron.
That is to say that matches in an exon region should have be given a higher weighting than matches in intronic regions.
Also, when a read pair maps to 2 exons, the insert size should be more flexible as the intron length can be vary among different mammals. Since the library insert is less than 2kb for short libraries, the more common situation should be one read on exon and another on intron.
This is different from RNA-seq as I am using WGS data of a whole genome, so both exons and introns are in the reads. And I want to align them to a human reference sequence.