ssaha and bwa-sw vs. bowtie/bwa...etc

[BioSlayer]

For an educational and practical perspective, the question here has been teasing me for a satisfying answer as it has been a subject of a lengthy discussion between my superiors and I was pushed into it to give them a satisfying answer.

Let's have this simplistic background; If we make a distinction between Sanger and NGS sequencing techniques that the main difference is that the later is hugely parallel (fastq files for both techniques can be obtained). And if we make another distinction between short read and long read mapping tools and that the later aren't hash based and employed in analyzing NGS platforms data but not that data produced by traditional Sangers (capillary based sequencing).

Now, the question is, given that the fastq files generated by either NGS or Sanger platforms will still have quality scores that are phred based, what essential differences exist if I use bowtie for example to map sequences produced by a sanger platform ? (if those sequences were shorter than 200 nts)

Choosing an appropriate mapping tool is paramount of course however, I don't fully comprehend why I will have to say use SSAHA2 on Sanger data as opposed to the faster bowtie...