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 qualityTRAILING: Cut bases off the end of a read, if below a threshold qualityCROP: Cut the read to a specified lengthHEADCROP: Cut the specified number of bases from the start of the readMINLEN: Drop the read if it is below a specified lengthTOPHRED33: Convert quality scores to Phred-33TOPHRED64: Convert quality scores to Phred-64It 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.

Version: 0.39

Availability: GALILEO100, MARCONI

Target: all

Official web site:

Related Commands:

How to use:

module load profile/bioinf
module load trimmomatic

java -jar $TRIMMOMATIC_HOME/bin/trimmomatic-0.39.jar

Help and Documentation:

For more information, visit the documentation site: