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  • Trimmomatic: A flexible read trimming tool for Illumina NGS data

Trimmomatic: A flexible read trimming tool for Illumina NGS data

http://www.usadellab.org/cms/?page=trimmomatic

Paired End:

java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This will perform the following:

  • Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
  • Remove leading low quality or N bases (below quality 3) (LEADING:3)
  • Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
  • Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
  • Drop reads below the 36 bases long (MINLEN:36)

More at http://www.usadellab.org/cms/?page=trimmomatic