2.9 years ago
Although many use that way, blat is not the best choice when there are many gaps. Firstly, blat does not use Smith-Waterman to refine the alignment. It does not generate the best alignment and you cannot get something equivalent to CIGAR from PSL. Secondly, blat is designed for EST alignment in mind. Sometimes it produces spurious split alignment while a better alignment is present. Blat is probably the first whole-genome cDNA aligner. It is not really an alternative to blast. SSAHA2 is.
The strength of blast/blat/ssaha2 is that they can give an exhaustive list of local hits for long and diverged sequences. The list is very helpful to investigate problems. It also gives users more control over what to accept. However, they are slower also because of this. Most recent fast long-read aligners do not attempt to go through all the local hits.
PS: bwa/bowtie1 are not general-purpose aligners. They designed for short reads only. Bwa-sw is more tuned for general purpose, but it does not output multiple hits. Bowtie2, I think, cannot output an exhaustive list local hits as blast/blat/ssaha2 does, either. It does not work very well with chimeric alignment. No aligners so far are good for everything. Choose based on your needs.
PSS: Blat/ssaha2 are good for Sanger reads, but they are very slow for >10kb sequences. For that long sequences, you need others designed for genome-to-genome or assembly-to-genome alignment.