Trimmomatic

1 Overview | 2 Using | 2.1.1 Multicore: | 2.2 Adapters:

Overview

Trimmomatic is a flexible read trimming tool for Illumina NGS data.

Using

Use the module name trimmomatic to discover versions available and to load the application.

ARCC has created a wrapper script to make using the commands easier so you simply need to use the trimmomatic call from the command-line:

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

[]$ trimmomatic PE -version
0.39

Multicore:

The trimmomatic command can be ran with multiple threads. Run the trimmomatic call from the command-line to see details on the -threads option.

Example:

[]$ salloc -A arcc -t 1:00:00 -c 16

[@m001 trimmmomatic] trimmomatic PE -threads 16 \
    data/SRR2589044_1.fastq.gz data/SRR2589044_2.fastq.gz \
    SRR2589044_1.trim.fastq.gz SRR2589044_1un.trim.fastq.gz \
    SRR2589044_2.trim.fastq.gz SRR2589044_2un.trim.fastq.gz \
    SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:40:15

Adapters:

Adapters are available at the trimmomatic Git Hub.

On Beartooth and medicineBow, the following adapters are available, and can be copied from: /apps/u/opt/linux/trimmomatic/0.39/adapters/

NexteraPE-PE.fa TruSeq2-PE.fa TruSeq2-SE.fa TruSeq3-PE-2.fa TruSeq3-PE.fa TruSeq3-SE.fa