{"id":4408,"date":"2020-01-10T14:02:59","date_gmt":"2020-01-10T14:02:59","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4408"},"modified":"2020-01-10T16:24:45","modified_gmt":"2020-01-10T16:24:45","slug":"trimmomatic","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/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, 0.35, 0.36 and 0.39 are 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

All users may access and use Trimmomatic. The software is open source using the GPL3 license. Users should consult the following file for further information:<\/p>\n

$TRIMMOMATIC_HOME\/doc\/LICENSE<\/pre>\n
For citation information see the Trimmomatic website<\/a>.<\/p>\n
Set up procedure<\/h2>\n
The Trimmomatic adapter files can be found under the directory $TRIMMOMATICSHARE\/adapters\/<\/p>\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
$TRIMMOMATIC_JAVA_TMPDIR\r\n$TRIMMOMATICSHARE\r\n$TRIMMOMATIC_JAVA_MEM_MX<\/pre>\n
Running the application<\/h2>\n
Please do not run trimmomatic commands on the login node. Computationally intense work should be done via the batch system.<\/p>\n
It can be run in single or paired end mode. A wrapper has been included you you don’t need to run the java command.<\/p>\n
single<\/h5>\n
java -jar $TRIMMOMATIC_JAVA\/trimmomatic.jar SE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> <output> <step 1> ...\u200b<\/pre>\n
paired<\/h5>\n
java -jar <$TRIMMOMATIC_JAVA\/trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...<\/pre>\n
Examples<\/h3>\n
Serial batch submission<\/h4>\n
#!\/bin\/bash\u00a0 --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\nmodule load apps\/binapps\/trimmomatic\/0.39\r\n\r\ntrimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log<\/pre>\n
Note that the\u00a0$NSLOTS<\/code>\u00a0variable will be set automatically to\u00a01<\/code>\u00a0by the batch system. This ensure trimmomatic uses only a single core, matching the single core you\u2019ve reserved by using a serial jobscript.<\/p>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where\u00a0scriptname<\/em>\u00a0is the name of your jobscript.<\/p>\n
Parallel batch submission<\/h4>\n
#!\/bin\/bash\u00a0 --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 8 # Example: 8 cores. Can specify 2-32. Do NOT use 1\r\nmodule load apps\/binapps\/trimmomatic\/0.39\r\n\r\ntrimmomatic --threads $NSLOTS SE in.fq out.fq OPERATION [OPERATION...] > out.log<\/pre>\n
Note that\u00a0$NSLOTS<\/code>\u00a0will be set automatically to the number of cores requested on the\u00a0#$ -pe<\/code>\u00a0line. 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\u00a0scriptname<\/em>\u00a0is the name of your jobscript.<\/p>\n
Further info<\/h2>\n