Purdue University

Commands

• skewer

Module

You can load the modules by:

module load biocontainers
module load skewer

Example job

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 Skewer on our clusters:

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

module --force purge
ml biocontainers skewer

skewer -l 50 -m pe -o skewerQ30 --mean-quality 30 \
     --end-quality 30 -t 10 -x TruSeq3-PE.fa \
     input_1.fastq input_2.fastq