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 following versions of Trimmomatic are available on OSC clusters:
| Version | Owens | Pitzer |
|---|---|---|
| 0.36 | X* | |
| 0.38 | X* |
You can use module spider trimmomatic to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Trimmomatic is available to all OSC users. If you have any questions, please contact OSC Help.
http://www.usadellab.org/cms/?page=trimmomatic, Open source
module load trimmomatic. The default version will be loaded. To select a particular Trimmomatic version, use module load trimmomatic/version. For example, use module load trimmomatic/0.36 to load Trimmomatic 0.36.This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.
From module load trimmomatic, a new environment variable, TRIMMOMATIC, will be set.
Thus, users can use the software by running the following command: java -jar $TRIMMOMATIC {other options}.
module load trimmomatic. The default version will be loaded. To select a particular Trimmomatic version, use module load trimmomatic/version. For example, use module load trimmomatic/0.38 to load Trimmomatic 0.38.This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.
From module load trimmomatic, a new environment variable, TRIMMOMATIC, will be set.
Thus, users can use the software by running the following command: java -jar $TRIMMOMATIC {other options}.