trimmomatic
Link to section 'Introduction' of 'trimmomatic' Introduction
Trimmomatic is a flexible read trimming tool for Illumina NGS data.
For more information, please check its website: https://biocontainers.pro/tools/trimmomatic.
Link to section 'Versions' of 'trimmomatic' Versions
- 0.39
Link to section 'Commands' of 'trimmomatic' Commands
- trimmomatic
Link to section 'Module' of 'trimmomatic' Module
You can load the modules by:
module load biocontainers
module load trimmomatic
Link to section 'Example job' of 'trimmomatic' 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 Trimmomatic on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=trimmomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers trimmomatic
trimmomatic PE -threads 8 \
input_forward.fq.gz input_reverse.fq.gz \
output_forward_paired.fq.gz output_forward_unpaired.fq.gz \
output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36