Advanced options: to align very short reads - pb-cdunn/blasr GitHub Wiki

Blasr is designed to align pacbio long reads to references. Blasr, with default parameters, is not tailed for aligning very short reads. In order to align short reads, you may want to try:

$ blasr short_reads.fa ref.fa -minMatch 8 -minSubreadLength 1 -minReadLength 1 -maxScore 200