Trimmomatic

module avail trimmomatic/

Trimmomatic is 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.

Trimmomatic works with FASTQ files. Files compressed using either gzip or bzip2 are supported, and are identified by use of .gz or .bz2 file extensions.

Usage

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 .