# blasr

## Summary

+ **Module Name:** blasr
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://github.com/PacificBiosciences/blasr](https://github.com/PacificBiosciences/blasr)

## Software Description

BLASR: The PacBio long read aligner BLASR is available on the lab
cluster.
## General Linux

    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