HPC:Trimmomatic
From HPC wiki
Trimmomatic
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
[asrini@node107 ~]$ java -jar /opt/software/Trimmomatic/0.32/trimmomatic-0.32.jar
Usage:
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...
