Running and Verifying fastp

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the directory where the test case is stored:

   cd /path/to/FASTP/testdata

3. Run the following commands to decompress the case files:

   gzip -d ERR1044518_1.fastq.gz
   gzip -d ERR1044518_2.fastq.gz

4. Run the following commands to run the test case:

   { time fastp -i ERR1044518_1.fastq -I ERR1044518_2.fastq -w 16 ; } 2>&1 |tee fastp.log

   After the command is executed, the following information is displayed:

   Duplication rate: 0.581538%
   Insert size peak (evaluated by paired-end reads): 169
   JSON report: fastp.json
   HTML report: fastp.html

   

   fastp supports multi-thread running. -w specifies the number of threads, a maximum of 16 allowed.

   After the command is executed, the fast.json and fast.html reports are generated. You can use the -j and -h parameters to specify the paths and names of the two files, respectively.

   To view more parameter information, run the fastp --help command.