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trimmomatic
Overview
Trimmomatic is a program to perform a variety of useful trimming tasks for Illumina paired-end and single ended data.
Versions 0.32 and 0.36 is installed.
Restrictions on use
Trimmomatic is licensed under the GNU General Public License version 3; there are no restrictions on its use.
Set up procedure
To access the software you must first load one of the modulefiles:
module load apps/binapps/trimmomatic/0.36
Environment variables
The modulefile defines a number of environment variables that can be used to access data files and modify the behaviour of the program:
TRIMMOMATIC_JAVA_TMPDIR=/tmp TRIMMOMATICSHARE=/opt/gridware/pkg/apps/trimmomatic/0.32/noarch/share TRIMMOMATIC_JAVA_MEM_MX=2g
The Trimmomatic adapter files can be found under the directory $TRIMMOMATICSHARE/adapters/
Running the application
Please do not run Trimmomatic on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings trimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log
Note that the $NSLOTS variable will be set automatically to 1 by the batch system. This ensure trimmomatic uses only a single core, matching the single core you’ve reserved by using a serial jobscript.
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Example: 8 cores. Can specify 2-16. Do NOT use 1. trimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log
Note that $NSLOTS will be set automatically to the number of cores requested on the #$ -pe line. This ensures the trimmomatic uses only the cores you have reserved in the batch system.
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.