Trimmomatic-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.36

Author / Distributor

Trimmomatic

Description

"Trimmomatic 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." More details are at Trimmomatic

Running Program

The last version of this application is at /usr/local/apps/eb/Trimmomatic/0.36-Java-1.8.0_144

To use this version, please load the module with

ml Trimmomatic/0.36-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_Trimmomatic
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Trimmomatic.%j.out
#SBATCH --error=Trimmomatic.%j.err

cd $SLURM_SUBMIT_DIR
ml Trimmomatic/0.36-Java-1.8.0_144
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Trimmomatic/0.36-Java-1.8.0_144 
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar -h

Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version

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Installation

Source code is obtained from Trimmomatic

System

64-bit Linux