722  fastqc Ath_tae_CTTGTA_L003_R2_010.fastq
  723  cd ./1/
  724  java -jar /usr/share/java/trimmomatic.jar SE 1.fastq out1.fastq ILLUMINACLIP:NexteraPE-PE.fa:2:7:7
  725  java -jar /usr/share/java/trimmomatic.jar SE out1.fastq out2.fastq ILLUMINACLIP:TruSeq2-PE.fa:2:7:7
  726  java -jar /usr/share/java/trimmomatic.jar SE out2.fastq out3.fastq ILLUMINACLIP:TruSeq2-SE.fa:2:7:7
  727  java -jar /usr/share/java/trimmomatic.jar SE out3.fastq out4.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:7:7
  728  java -jar /usr/share/java/trimmomatic.jar SE out4.fastq out5.fastq ILLUMINACLIP:TruSeq3-PE-2.fa:2:7:7
  729  java -jar /usr/share/java/trimmomatic.jar SE out5.fastq out6.fastq ILLUMINACLIP:TruSeq3-SE.fa:2:7:7
  730  java -jar /usr/share/java/trimmomatic.jar SE out6.fastq out7.fastq TRAILING:20
  731  java -jar /usr/share/java/trimmomatic.jar SE out7.fastq out8.fastq MINLEN:50
  732  fastqc out8.fastq