I recently used exonerate to align PacBio Iso-Seq SMRT reads. Although this worked, it was very slow, and the data sets I had were pretty small (only about 3400 reads). I now have new, much larger data sets (~70,000 reads) and exonerate is just not cutting it. I have to split the fasta files up so as not to exhaust memory usage and even then the alignments runs for weeks. I am wondering if there are other, more efficient alignerd for these Iso-Seq SMRT reads. For example, does pbalign support long read alignment. i also found rHAT and a hacked version of STAR both on the PacBio GitHub. Has anyone used these options or does anyone have an alternative.
Thank you Harry