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.
module avail trimmomatic/ # list available modules module load trimmomatic # load (default) module
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 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf