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Trimmomatic

Table of Contents

Introduction

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.  See the Software_Versions tab for a list of systems on which the software has been installed.

Running Trimmomatic on Breezy

To run Trimmomatic on Breezy, in your batch job script, initialize your envionment to use Java, specify the Trimmomoatic jar file location and match the number of threads to use with the number of cores requested of the batch job system by using the PBS_NUM_PPN environment variable. 

#PBS -l nodes=1:ppn=1
module load java
JAR=/global/software/trimmomatic/Trimmomatic-0.36/trimmomatic-0.36.jar
java -jar $JAR -threads ${PBS_NUM_PPN} <other Trimmomatic options>

On Breezy, the number speified for ppn can be as large as 24, but, as of this writing (2016-08-08) we have not tested Trimmomatic and do not know how many threads it can effectively use.

Running Trimmomatic on Hungabee

To run Trimmomatic on Hungabee, initialize your envionment with:

module load application/trimmomatic/0.33

and then choose the paired-end option:

java org.usadellab.trimmomatic.TrimmomaticPE ...

or single-end option:

java org.usadellab.trimmomatic.TrimmomaticSE ...

2016-08-08 - Added Breezy entry.

System Jasper Breezy Hungabee
Version 0.36 0.36 0.33