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Thursday, December 7, 2017
BLASR: The PacBio® long read aligner
BLASR is available on the lab cluster.
module load 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