Blasr

Introduction

Blasr Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment.

For more information, please check its website: https://biocontainers.pro/tools/blasr and its home page on Github.

Versions

5.3.5

Commands

blasr

Module

You can load the modules by:

module load biocontainers
module load blasr

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Blasr on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=blasr
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers blasr

blasr reads.bas.h5  ecoli_K12.fasta -sam