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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.

The current trimming steps are:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.

SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.

LEADING: Cut bases off the start of a read, if below a threshold quality

TRAILING: Cut bases off the end of a read, if below a threshold quality

CROP: Cut the read to a specified length

HEADCROP: Cut the specified number of bases from the start of the read

MINLEN: Drop the read if it is below a specified length

TOPHRED33: Convert quality scores to Phred-33

TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.

For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.

Required Modules


  • trimmomatic

System Variables


Additional Information

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 \


  • Validate 4/5/2018