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.
Availability and Restrictions
Versions
The following versions of Trimmomatic are available on OSC clusters:
| Version | Pitzer | Ascend |
|---|---|---|
| 0.38 | X* | 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.
Access
Trimmomatic is available to all OSC users. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
http://www.usadellab.org/cms/?page=trimmomatic, Open source
Usage
Usage on Pitzer
Set-up
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.Usage
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}.
Usage on Ascend
Set-up
module load trimmomatic/version. For example, use module load trimmomatic/0.38 to load Trimmomatic 0.38.Usage
This software provides a wrapper script around a Java executable .jar file. To see the usage, use the following command: trimmomatic. The script uses the variables $JAVA_ARGS and $JAVA_OPTS. You can set these as environment variables to modify the java arguments, either before invoking the trimmomatic script or on the same line: JAVA_ARGS="some_args" trimmomatic
