Mapping commands
# human-readable output
blasr reads.bas.h5 ecoli_K12.fasta -m 0
# SAM output with or without soft-clipping
blasr reads.bas.h5 ecoli_K12.fasta -sam
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
# multiple threads
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
# Faster, but less sensitive
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
References
Manual
https://github.com/PacificBiosciences/blasr/wiki
Github
https://github.com/PacificBiosciences/blasr https://github.com/PacificBiosciences/blasr/wiki/Blasr-Output-Format
Website
http://bix.ucsd.edu/projects/blasr/
Paper
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-238