Trimmomatic过滤Illumina低质量序列

1. 下载安装

直接去官网下载二进制软件,解压后的trimmomatic-0.36.jar即为我们需要的软件

官网：

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

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip

unzip Trimmomatic-0.38.zip

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
unzip Trimmomatic-0.36.zip 

[Trimmomatic-0.38]# tree
.
├── adapters
│   ├── NexteraPE-PE.fa
│   ├── TruSeq2-PE.fa
│   ├── TruSeq2-SE.fa
│   ├── TruSeq3-PE-2.fa
│   ├── TruSeq3-PE.fa
│   └── TruSeq3-SE.fa
├── LICENSE
└── trimmomatic-0.38.jar
 

2. 运行软件

一般我们使用默认参数运行即可，具体使用方法可参见官网http://www.usadellab.org/cms/?page=trimmomatic
使用默认参数运行程序:

sudo java -jar trimmomatic-0.36.jar PE 
  -phred33 ~/SRR733/SRR2854733_1.fastq ~/SRR733/SRR2854733_2.fastq 
   ~/SRR733/clsseq/SRR2854733_1_paired.fq ~/SRR733/clsseq/SRR2854733_1_unpaired.fq 
   ~/SRR733/clsseq/SRR2854733_2_paired.fq ~/SRR733/clsseq/SRR2854733_2_unpaired.fq 
   ILLUMINACLIP:/usr/local/src/Trimmomatic/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 
   LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:8 MINLEN:36

运行结果：

Input Read Pairs: 23396043 
Both Surviving: 20842668 (89.09%) 
Forward Only Surviving: 2537100 (10.84%) 
Reverse Only Surviving: 13969 (0.06%) 
Dropped: 2306 (0.01%)
TrimmomaticPE: Completed successfully

3. 常用参数说明

PE/SE
    设定对Paired-End或Single-End的reads进行处理，其输入和输出参数稍有不一样。
-threads
    设置多线程运行数
-phred33
    设置碱基的质量格式，可选pred64
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10
    切除adapter序列。参数后面分别接adapter序列的fasta文件：允许的最大mismatch数：palindrome模式下匹配碱基数阈值：simple模式下的匹配碱基数阈值。
LEADING:3
    切除首端碱基质量小于3的碱基
TRAILING:3
    切除尾端碱基质量小于3的碱基
SLIDINGWINDOW:4:15
    从5'端开始进行滑动，当滑动位点周围一段序列(window)的平均碱基低于阈值，则从该处进行切除。Windows的size是4个碱基，其平均碱基
质量小于15，则切除。
MINLEN:50
    最小的reads长度
CROP:<length>
    保留reads到指定的长度
HEADCROP:<length>
    在reads的首端切除指定的长度
TOPHRED33
    将碱基质量转换为pred33格式
TOPHRED64
    将碱基质量转换为pred64格式

Question: Which truseq trimmomatic adapters file to use when removing truseq adapters?

It depends mostly on which TruSeq protocol was used (V2 - which is old at this stage and usually data from the GAII, or V3, which is everything from the HiSeq or later machines), and whether the data is single-ended or paired ended (SE or PE). The only exception is TruSeq-3-PE which has two sets - TruSeq-3-PE.fa works fine for high quality libraries, but TruSeq-3-PE-2.fa contains some additional sequences which find partial adapters in unusual location/orientation.

ref：

https://www.jianshu.com/p/7b5591673255

https://www.biostars.org/p/323087/