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Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters. It 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. Trimmomatic version 0.32 is installed across all HPC nodes and is made available via a module file.

[asrini@node107 ~]$ module load Trimmomatic-0.32

The above module load command sets the $TRIM_JAR environment variable.

[asrini@node107 ~]$ echo $TRIM_JAR 

This environment variable can be used by passing it directly to the java command:

[asrini@node107 ~]$ java -jar $TRIM_JAR 
       PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
       SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...

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