blasr

Module Name

blasr

Last Updated On

08/29/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

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

Default

1.3.1

Other Modules

1.3.1, 5.3.5

Default

1.3.1

Other Modules

1.3.1, 5.3.5

Default

1.3.1

Other Modules

1.3.1, 5.3.5