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Bioinformatics - Trimmomatic

Instructions on how to run (and, if needed, install a customized version of) Trimmomatic

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

  1. Running Trimmomatic on Thunder
  2. Install customized Trimmomatic on Thunder
Please refer to the CCAST User Guide and the the article Running Bioinformatics Software on HPC Clusters for general information about using CCAST resources and running bioinformatics software on CCAST's HPC clusters.

1. Running Trimmomatic on Thunder


Example: Quality control and adapter trimming on NGS sequences


Location: /gpfs1/projects/ccastest/training/examples/Trimmomatic_example


File list

· trimmomatic_job.pbs: job submission script   

· EGL290_S65_L001_R1_001.fastq: paired-end sequences in fastq format

· EGL290_S65_L001_R2_001.fastq: paired-end sequences in fastq format


Steps

· Copy example directory to your SCRATCH directory

o    cp -r /gpfs1/projects/ccastest/training/examples/Trimmomatic_example $SCRATCH

· Go to the copied directory

o    cd  $SCRATCH/Trimmomatic_example

· Edit the job submission script as needed, then submit the job

o    qsub trimmomatic_job.pbs


2. Install Customized Trimmomatic on Thunder

Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.

Summary

(a) Require a suitable Java Runtime Environment; (available via “module load java/jdk”) 

(b) It includes a directory of adapter sequences that one may use in the command.

Details

In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME is your username on Thunder.


(a) Install and set path

·       Go to the SOFTWARE directory: 

o    "cd /gpfs1/home/USERNAME/SOFTWARE

·       Download and unzip trimmomatic: 

o    "wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip

·       "unzip Trimmomatic-0.39.zip"

(b) Test

·       Go to the scratch directory: 

o    "cd /gpfs1/scratch/USERNAME

·       Download and unzip sample data: (Only use some of them, as same as the one used in fastqc test)

o    "wget http://de.cyverse.org/dl/d/C4416643-CA5C-4CDD-9FB0-86520AB61059/example_reads.tar.gz

o    "tar -zxvf example_reads.tar.gz"

·       Make, go to test directory and copy data samples: 

o    "mkdir trimmomatic_example"

o    "cd trimmomatic_example"

o    "cp /gpfs1/home/USERNAME/SOFTWARE/example_reads/*S65* ."

·       Write and submit the job 

o    "qsub trimmomatic_job.pbs

--------------- trimmomatic_job.pbs -----------------

#!/bin/bash

#PBS -q default

#PBS -N Trimmomatic_test

#PBS -l select=1:mem=10gb:ncpus=4

#PBS -l walltime=1:00:00

## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”

#PBS -W group_list=x-ccast-prj

cd $PBS_O_WORKDIR

# Set path for Trimmomatic root directory

export TRIMMOMATIC_HOME=/gpfs1/home/USERNAME/SOFTWARE/Trimmomatic-0.39

java -jar $TRIMMOMATIC_HOME/trimmomatic-0.39.jar PE -phred33 -threads $NCPUS EGL290_S65_L001_R1_001.fastq EGL290_S65_L001_R2_001.fastq output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:$TRIMMOMATIC_HOME/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3SLIDINGWINDOW:4:15 MINLEN:36

exit 0

  

See Also:




Keywords:ccast, hpc, thunder, bioinformatics, trimmomatic   Doc ID:108086
Owner:Liu Y.Group:IT Knowledge Base
Created:2020-12-27 12:02 CDTUpdated:2020-12-29 02:08 CDT
Sites:IT Knowledge Base
CleanURL:https://kb.ndsu.edu/trimmomatic
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