trimmomatic

adapter:

/home/shen/miniconda3/share/trimmomatic-0.38-1/adapters

可以寻找:

find ./ -name TruSeq3-PE.fa

单端:

trimmomatic SE -phred33 -threads 10 sp.fq sp.trimmed.fq ILLUMINACLIP:/home/pc/miniconda3/pkgs/trimmomatic-0.38-1/share/trimmomatic-0.38-1/adapters/TruSeq3-SE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 AVGQUAL:20 MINLEN:36

双端:

trimmomatic PE -phred33 -threads 20 ctr.R1.fq ctr.R2.fq ctr.R1.paired.fq ctr.R1.unpaired.fq ctr.R2.paired.fq ctr.R2.unpaired.fq ILLUMINACLIP:/home/pc/miniconda3/pkgs/trimmomatic-0.38-1/share/trimmomatic-0.38-1/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 AVGQUAL:20 MINLEN:36

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