Which software is proper for pacbio reads alignment to reference genome? I see bwa mem is ok, and there is blasr, but slow. How about MHAP? But from the manual it says the output is blasr m4 format, not sam/bam. Why that? The MHAP paper show better alignment performance to blasr, but it cannot generate sam?
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Blasr is the recommended option, but as you noted, can be slow. Take a look at some of these tips to speed it up a little bit for nearly identical sequences:Originally posted by Rui Guo View Post
mhap is another option, but as you noted, output is not in SAM format.
The third option would be 'daligner' which is pretty fast, but also uses it's own output format (*.las) which is not what you asked for, but one of our preferred methods for aligning long reads back to a reference. See Gene Meyer's Dazzlerblog for details:
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