Trimmomatic

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

The following versions of Trimmomatic are available on OSC clusters:

Version Oakley Owens
0.36 X* X*
*: Current default version

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 without restriction.

Usage on Oakley

Set-up

To configure your environment for use of Trimmomatic, run the following command:   module load trimmomati. 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.

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 Owens

Set-up

To configure your environment for use of Trimmomatic, run the following command:   module load trimmomati. 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.

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}

Further Reading

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