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## Running BLASR
Typing 'blasr -h' or 'blasr -help' on the command line will give you a
list of options. At the least, provide a fasta, fastq, or bas.h5 file,
and a genome.
### Some typical use cases
Align reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
blasr reads.bas.h5 ecoli_K12.fasta -sam
Same as above, but with soft clipping
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
Use multiple threads
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
Include a larger minimal match, for faster but less sensitive alignments
blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
Produce alignments in a pairwise human readable format
blasr reads.bas.h5 ecoli_K12.fasta -m 0
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
Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.
sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt
blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt
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