Trimmomatic

Introduction

Another tool for quality trimming ... this is probably the best known.

Usage

Trimmomatic is quite unique in the way it is called.

It is a java program, so this requires the jar file naturally, and then:

1. whether single- or pair-end reads (SE|PE)
2. number of threads with hyphen, i.e. -threads N
3. whether quality scoring is phred33 or phred64 (although it will try to detect)

• $TS3SE is TruSeq3-SE.fa
• $TS2SE is TruSeq2-SE.fa
• $TS2PE is TruSeq2-PE.fa
• $NXPE is NexteraPE-PE.fa
• $TS3PE is TruSeq3-PE.fa
• $TS3PE2 is TruSeq3-PE-2.fa

Example use-cases

java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50