trimmomatic的介绍

trimmomatic的官网trimmomatic
trimmomatic可以对测序数据进行过滤
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:$file_path/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

运行上面的命令可以完成以下任务
Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10) #去掉接头
Remove leading low quality or N bases (below quality 3) (LEADING:3) #去掉开头质量低于3或N碱基
Remove trailing low quality or N bases (below quality 3) (TRAILING:3) #去掉末尾质量低于3或N碱基
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15) #以4个碱基为滑动窗口对reads进行扫描，当平均质量值低于15时进行剪切
Drop reads below the 36 bases long (MINLEN:36) #去掉长度小于36的reads