Trimmomatic

Introduction

Trimmomatic is a tool used for trimming Illumina sequencing data. It handles adapter removal, quality trimming, dropping short reads, and other quality control steps before alignment or quantification. It is usually a standard tool that is ran, if found necessary, after evaluating the QC reports (FastQC or MultiQC).

Requirements

Trimmomatic is available as a module on NCSA servers. Therefore, requirements are loaded automatically:

module load trimmomatic

Usage

Below is a code snippet that can be used to create a simple SLURM batch script for trimming paired-end FASTQ files. Adjust input/output file names and adapter paths as needed.

# Path to Working Directory

myWorkDir="/path/to/my/working/directory"
cd $myWorkDir

## -- Reserve a folder with your raw FASTQ files, e.g.:
## -- $myWorkDir/samples/sample1_R1.fastq.gz and $myWorkDir/samples/sample1_R2.fastq.gz
## -- Reserve a folder for trimmed outputs:
## -- $myWorkDir/trimmed/

mkdir -p $myWorkDir/trimmed

# Run Trommomatic
# Example for paired-end reads using built-in adapter file

trimmomatic PE \
    -threads 4 \
    $myWorkDir/samples/sample_R1.fastq.gz \
    $myWorkDir/samples/sample_R2.fastq.gz \
    $myWorkDir/trimmed/sample_R1.paired.fq.gz \
    $myWorkDir/trimmed/sample_R1.unpaired.fq.gz \
    $myWorkDir/trimmed/sample_R2.paired.fq.gz \
    $myWorkDir/trimmed/sample_R2.unpaired.fq.gz \
    ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS/NexteraPE-PE.fa \
    LEADING:5 \
    TRAILING:5 \
    SLIDINGWINDOW:4:15 \
    MINLEN:50

References

Bolger A.M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15):2114–2120.