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 ${NSLOTS} option must be used.
Serial job¶
Here is an example job running on 2 cores and 4GB of total memory, showing the paired-end example available on the Trimmomatic official documentation, linked in the references below:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
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 ${NSLOTS}