Trimmomatic: Reads Quality Control

软件简介

主要用于Illumina双端或单端测序数据的质控，基本原理是Sliding window。二代测序的扩增子测序和宏基因组测序用该方法都是可行的，我主要用来做宏基因组测序数据的质控。

参数列表

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
LEADING: Cut bases off the start of a read, if below a threshold quality
TRAILING: Cut bases off the end of a read, if below a threshold quality
CROP: Cut the read to a specified length
HEADCROP: Cut the specified number of bases from the start of the read
MINLEN: Drop the read if it is below a specified length
TOPHRED33: Convert quality scores to Phred-33
TOPHRED64: Convert quality scores to Phred-64

常用命令

java -jar /path/to/trimmomatic-0.39.jar PE \
    -threads 32 -phred33 \
    /path/to/rawread.R1.fq \
    /path/to/rawread.R2.fq \
    /path/to/rawread.trimmed.R1.fq \
    /path/to/rawread.unpaired.R1.fq \
    /path/to/rawread.trimmed.R2.fq \
    /path/to/rawread.unpaired.R1.fq \
    LEADING:3 TRAILING:3 MINLEN:50 SLIDINGWINDOW:4:20

相关参考链接

https://github.com/usadellab/Trimmomatic
https://www.jianshu.com/p/a8935adebaae