Software: Trim-galore
Description
Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files.
Available Versions
Unspecified: | 0.6.7 |
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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/.
Commands
- trim_galore
Module
You can load the modules by:
module load biocontainers
module load trim-galore
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 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