trimmomatic
Link to section 'Description' of 'trimmomatic' Description
A flexible read trimming tool for Illumina NGS data.
Link to section 'Versions' of 'trimmomatic' Versions
- Anvil: 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 trimmomatic
Link to section 'Example job' of 'trimmomatic' Example job
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 load 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