1. 基本命令 fastp -i in.R1.fq.gz -I in.R2.fq.gz # 单端测序# 双端测序fastp -i in.R1.fq.gz -I in.R2.fq.gz \ -o out.R1.fq.gz -O out.R2.fq.gz \ –detect_adapter_for_pe

注：

-a, –adapter_sequence               the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])

自动生成质控文件fastp.html和fastp.json，可以通过–html 和–json指定文件名字。

thread 默认为2，可以设定 -w, –thread ，最大为16

2.处理带UMI的fastq数据 fastp -i in.R1.fq.gz -I in.R2.fq.gz \ -o out.R1.fq.gz -O out.R2.fq.gz \ –umi \ –umi_loc per_read \ –umi_len 6 \ –umi_prefix UMI \ –umi_skip 4 \ –detect_adapter_for_pe

参数说明

     –umi  # enable umi                           
      –umi_loc  per_read  # read1和read2都有UMI
      –umi_len  6  # UMI序列长度
      –umi_prefix UMI  #UMI序列前缀
      –umi_skip 4  # UMI序列后要切除的碱基数

adapter相关参数

  -a, –adapter_sequence               the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])

      –adapter_sequence_r2            the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence> (string [=auto])

      –adapter_fasta                  specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=])

      –detect_adapter_for_pe          by default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.

其他filter参数一般用default。

参考

质控软件fastp常用参数说明_sinat_32872729的博客-CSDN博客_fastp

https://github.com/OpenGene/fastp