BLASR

module load blasr

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