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