Usage

Use the trimmomatic_se and trimmomatic_pe wrappers for trimmomatic/0.22 to run Trimmomatic for single-end and paired-end reads respectively or the trimmomatic wrapper for trimmomatic/0.32 or later.

For example:

module load trimmomatic/0.32
trimmomatic PE --phred33 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:${HPC_TRIMMOMATIC_ADAPTER}/TruSeq3-PE.fa:2:30:10 
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36