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Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process. Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used). Files compressed using either „gzip‟ or „bzip2‟ are supported, and are identified by use of „.gz‟ or „.bz2‟ file extensions.




Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of trimmomatic and load default version of trimmomatic as

module avail trimmomatic/ # list available modules
module load trimmomatic   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail trimmomatic

and choose explicit version you want to use.

There is defined an environment variable TRIMMOMATIC_BIN which points to the program jar file. Example of running:

java -jar /software/trimmomatic-0.32/dist/jar/trimmomatic-0.32.jar
java -jar /software/trimmomatic/0.36/dist/jar/trimmomatic-0.36.jar
java -jar /software/trimmomatic/0.39/trimmomatic-0.39/Trimmomatic-0.39/trimmomatic-0.39.jar
If you do not need to set any special parameters to java, you can use the available alias to above command called trimmomatic .


Documentation is in file /software/trimmomatic-0.32/doc/TrimmomaticManual_V0.32.pdf