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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 reads and a genome, where reads file format can be
bam|dataset|fasta|fastq|bas.h5, and genome file format can be fasta|ReferenceSet.
### Some typical use cases
Align subreads in movie.subreads.bam to ecoli_K12 genome, and output in BAM format.
blasr movie.subreads.bam ecoli_K12.fasta --bam --out alignments.bam
Align subreads in movie.subreadset.xml to ecoli_K12 genome, and output in BAM format.
blasr movie.subreadset.xml ecoli_K12.fasta --bam --out alignments.bam
Align subreads in movie.subreadset.xml to ecoli_K12 genome ReferenceSet, and output in BAM format.
blasr movie.subreadset.xml ecoli_K12.referenceset.xml --bam --out alignments.bam
Align CCS reads in movie.consensusreadset.xml to ecoli_K12 genome, and output in BAM format.
blasr movie.consensusreadset.xml ecoli_K12.fasta --bam --out alignments.bam
Use multiple threads, e.x., 16 threads
blasr movie.subreads.bam ecoli_K12.fasta --nproc 16
Include a larger minimal match, for faster but less sensitive alignments
blasr movie.subreads.bam ecoli_K12.fasta --minMatch 15
Produce alignments in a pairwise human readable format
blasr movie.subreads.bam ecoli_K12.fasta -m 0
Use a precomputed suffix array for faster startup
sawriter ecoli_K12.fasta.sa ecoli_K12.fasta #First precompute the suffix array
blasr movie.subreads.bam ecoli_K12.fasta --sa ecoli_K12.fasta.sa
Align RSII reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
blasr reads.bas.h5 ecoli_K12.fasta --sam --out alignments.sam
Same as above, but with soft clipping
blasr reads.bas.h5 ecoli_K12.fasta --sam --clipping soft --out alignments.sam
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