Trimmomatic¶
Trimmomatic performs a variety of useful trimming tasks for Illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Trimmomatic is available as a module on Apocrita.
Usage¶
To run the default installed version of Trimmomatic, simply load the trimmomatic
module:
module load trimmomatic
For usage documentation, run trimmomatic -help.
Example job¶
Core Usage
To ensure that Trimmomatic uses the correct number of cores, the
-threads ${SLURM_NTASKS} option must be used.
Serial job¶
Here is an example job running on 2 cores and 4GB of total memory, showing the paired-end example available on the Trimmomatic official documentation, linked in the references below:
#!/bin/bash
#SBATCH -n 2 # (or --ntasks=2) Request 2 cores
#SBATCH --mem-per-cpu=2G # Request 2GB RAM per core
#SBATCH -t 1:0:0 # Request 1 hour runtime
module load trimmomatic
trimmomatic PE 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 \
-threads ${SLURM_NTASKS}