Trim-galore
Introduction
Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/trim-galore
Versions
0.6.10
0.6.7
Commands
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 -p PartitionName # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=trim-galore
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module purge
module load trim-galore/XXXX ### you can run *module avail trim-galore* to check all available versions
trim_galore --paired --fastqc --length 20 -o sample1_trimmed Sample1_1.fq Sample1_2.fq