Trimmomatic
去除adapter； 相关：trim_galore (Cutadapt + FastQC)
Install
conda install -c bioconda trimmomatic -y
Usage
PE
trimmomatic PE -phred33 E_R1.raw.fq.gz E_R2.raw.fq.gz E_R1.trimmed.fq.gz E_R1.U.fq.gz E_R2.trimmed.fq.gz E_R2.U.fq.gz SLIDINGWINDOW:4:15 MINLEN:75 -summary summary.txt -trimlog log.txt -threads 64 -quiet
SE
trimmomatic SE -phred33 raw.fq.gz trimmed.fq.gz SLIDINGWINDOW:4:15 MINLEN:75 -summary summary.txt -trimlog log.txt -threads 64 -quiet
常用参数设置
# Trimmomatic内置了常规接头文件，illumina系的常规测序仪下机数据不用输入此参数
# :<待剪切的adapter序列>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
ILLUMINACLIP:adapter.fa:2:30:10
# :<windowSize>:<requiredQuality>
SLIDINGWINDOW:4:15
# :<length>
MINLEN:75
详细参数描述请见: TrimmomaticManual
Result
outputFiles(PE): paired(trimmed) unpaired(U)
E_R1.trimmed.fq.gz *
E_R1.U.fq.gz
E_R2.trimmed.fq.gz *
E_R2.U.fq.gz
outputFiles(SE):
trimmed.fq.gz *
summary
Input Read Pairs: 500
Both Surviving Reads: 494
Both Surviving Read Percent: 98.80
Forward Only Surviving Reads: 3
Forward Only Surviving Read Percent: 0.60
Reverse Only Surviving Reads: 3
Reverse Only Surviving Read Percent: 0.60
Dropped Reads: 0
Dropped Read Percent: 0.00
trimlog:
SRR22097888.1 E100030723L1C001R00100000167 length=150 150 0 150 0
SRR22097888.1 E100030723L1C001R00100000167 length=150 150 0 150 0
SRR22097888.2 E100030723L1C001R00100000669 length=150 149 0 149 1
SRR22097888.2 E100030723L1C001R00100000669 length=150 150 0 150 0
SRR22097888.3 E100030723L1C001R00100000975 length=150 150 0 150 0
SRR22097888.3 E100030723L1C001R00100000975 length=150 150 0 150 0
SRR22097888.4 E100030723L1C001R00100020241 length=150 150 0 150 0
SRR22097888.4 E100030723L1C001R00100020241 length=150 135 0 135 15
SRR22097888.5 E100030723L1C001R00100026545 length=150 150 0 150 0
SRR22097888.5 E100030723L1C001R00100026545 length=150 149 0 149 1
......