1 、fastp软件的安装
wget http://opengene.org/fastp/fastp
chmod a+x ./fastp
2、数据质控
双端测序
/public/home/ZCH_luxm/software/fastp -i /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_1.fastq.gz -o /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_1clean1.fastq.gz -I /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_2.fastq.gz -O /public/home/ZCH_luxm/NCBI/2_fq/SRR13413579_2clean1.fastq.gz --compression 9
参数设定：
-z 5 设置gzip压缩级别，默认4,1~9 1快-9小
--json 设置输出json文件名
--html 设置输出html文件名
3、批量处理数据(以PBS作业提交服务器）
[ZCH_luxm@login NCBI]$ cat /public/home/ZCH_luxm/NCBI/fastp.pbs
#PBS
#PBS -N fastp
#PBS -l nodes=1:ppn=5
#PBS -q batch
#PBS -o /public/home/ZCH_luxm/NCBI
#PBS -e /public/home/ZCH_luxm/NCBI
#!/bin/bash
for i in 655 868 874 879 918 924;do
{
/public/home/ZCH_luxm/software/fastp -i /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_1.fastq.gz -o /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_1clean.fastq.gz -I /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_2.fastq.gz -O /public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}_2clean.fastq.gz -h public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}.hxml -j public/home/ZCH_luxm/NCBI/2_fq/SRR3823${i}.json
}
done
参考链接
https://github.com/OpenGene/fastp#or-download-binary-only-for-linux-systems-httpopengeneorgfastpfastp
https://www.jianshu.com/p/762601f91539
