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


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)

Adapter file specification

You can use an environmental variable for the adapter fasta file, because they have been set by the module and will point to the right place. Here is a list, the most commonly used one is $TS3PE.

  • $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 $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:$TS3PE:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50