Trim-galore

Introduction

Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files.

For more information, please check its website: https://biocontainers.pro/tools/trim-galore and its home page: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.

Versions

• 0.6.7

Commands

• trim_galore

Module

You can load the modules by:

module load biocontainers
module load trim-galore

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 Trim-galore on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=trim-galore
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trim-galore

trim_galore  --paired --fastqc --length 20 -o sample1_trimmed Sample1_1.fq Sample1_2.fq