{"id":4439,"date":"2018-02-19T11:34:55","date_gmt":"2018-02-19T11:34:55","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4439"},"modified":"2018-02-19T11:34:55","modified_gmt":"2018-02-19T11:34:55","slug":"trimmomatic","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/trimmomatic\/","title":{"rendered":"trimmomatic"},"content":{"rendered":"

Overview<\/h2>\n

Trimmomatic is a program to perform a variety of useful trimming tasks for Illumina paired-end and single ended data.<\/p>\n

Versions 0.32 and 0.36 is installed.<\/p>\n

Restrictions on use<\/h2>\n

Trimmomatic is licensed under the GNU General Public License version 3; there are no restrictions on its use.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one<\/strong> of the modulefiles:<\/p>\n

\r\nmodule load apps\/binapps\/trimmomatic\/0.36\r\n<\/pre>\n
Environment variables<\/h2>\n
The modulefile defines a number of environment variables that can be used to access data files and modify the behaviour of the program:<\/p>\n
TRIMMOMATIC_JAVA_TMPDIR=\/tmp\r\nTRIMMOMATICSHARE=\/opt\/gridware\/pkg\/apps\/trimmomatic\/0.32\/noarch\/share\r\nTRIMMOMATIC_JAVA_MEM_MX=2g\r\n<\/pre>\n
The Trimmomatic adapter files can be found under the directory $TRIMMOMATICSHARE\/adapters\/<\/p>\n
Running the application<\/h2>\n
Please do not run Trimmomatic on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\ntrimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log<\/pre>\n
Note that the $NSLOTS<\/code> variable will be set automatically to 1<\/code> by the batch system. This ensure trimmomatic uses only a single core, matching the single core you’ve reserved by using a serial jobscript.<\/p>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Example: 8 cores. Can specify 2-16. Do NOT use 1.\r\n\r\ntrimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log\r\n<\/pre>\n
Note that $NSLOTS<\/code> will be set automatically to the number of cores requested on the #$ -pe<\/code> line. This ensures the trimmomatic uses only the cores you have reserved in the batch system.<\/p>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n