Quality Trimming Via Trimmomatic

最新推荐文章于 2024-10-07 11:22:30 发布

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最新推荐文章于 2024-10-07 11:22:30 发布

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文章标签： java

原文链接：http://www.cnblogs.com/liuhui0622/p/4991391.html

版权

已经去除接头(adapter)

java -jar trimmomatic.jar PE -threads 20 -phred33 \
left.fastq.gz right.fastq.gz \
left.Paired.qtrim.fq.gz left.Unpaired.qtrim.fq.gz \
right.Paired.qtrim.fq.gz right.Unpaired.qtrim.fq.gz \
SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:36

### The current trimming steps are:
- Remove leading low quality or N bases (below quality 5) (LEADING:5) 
- Remove trailing low quality or N bases (below quality 5) (TRAILING:5) 
- Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 5 (SLIDINGWINDOW:4:5) 
- Drop reads below the 36 bases long (MINLEN:36)

cat left.Paired.qtrim.fq.gz left.Unpaired.qtrim.fq.gz > left.PwU.qtrim.fq
cat right.Paired.qtrim.fq.gz right.Unpaired.qtrim.fq.gz > right.PwU.qtrim.fq

转载于:https://www.cnblogs.com/liuhui0622/p/4991391.html