Trimmomatic

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.

The current trimming steps are:

• ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
• SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
• LEADING: Cut bases off the start of a read, if below a threshold quality
• TRAILING: Cut bases off the end of a read, if below a threshold quality
• CROP: Cut the read to a specified length
• HEADCROP: Cut the specified number of bases from the start of the read
• MINLEN: Drop the read if it is below a specified length
• TOPHRED33: Convert quality scores to Phred-33
• TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.

For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.

Installed version

The currently installed version of Trimmomatic on the cluster is 0.36.

Using Trimmomatic on the HPC cluster

If you want to use Trimmomatic on the cluster, you will have to load its corresponding module first. You can do this with the command:

module load Trimmomatic

A short description will appear:

To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar

Running the command without any options will display usage intructions for trimmomatic:

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