TopHat2 versus HISAT2 inner workings
I don't believe this statement is true:

To solve this issue, both TopHat2 and HISAT2 chop up the unmapped reads into around 25bp fragments.

TopHat2 did not support spliced alignment directly.  This is why it followed this general approach of chopping the read up into small parts, followed by &quot;contiguous&quot; alignment of the sub-reads.  Hisat2 / Hisat-genotype support spliced alignment directly insofar as they don't pre-partition the reads into small parts, but allow dynamic extensions of alignments across splice junctions (in a way similar to how STAR works).  This is generally a fundamentally better approach and is one reason, among many, why TopHat/TopHat2 have been put into maintenance-only mode and have been officially superseded by Hisat2/genotype.