Blasr is my favorite aligner for multitude of reason – m option is very powerful in getting the exact formatting of output I need (finally someone agrees that length of the both query and reference should be included in the output:), SAM is also an option and reporting only best n hits is very convenient.

-bestn n (10)

               Report the top ‘n’ alignments.

When you use blasr often, it’s good idea to index the reference. However, one needs to (redundantly) provide link to both reference and index.

• Use a precomputed suffix array for faster startup
  • > sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array
  • > blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa

https://github.com/PacificBiosciences/blasr