The objective

Caculate the mean read length of Paired end fastq files

Getting started

To get started on using the scripts, the overarching directory PE_read, which contains all the needed files, scripts and directories. User need to change the path(work_dir) in Setting.txt. And run the command below on server or in terminal.

python3.7 readlength.py Setting.txt

Lay-out of directories and files.

users need to store data in the layout shown as below. (See test data)

• readlength.py

• Setting.txt

• testdata

  • Paired_end_fastq_files1

    • Read_1_fastq

    • Read_2_fastq

  • Paired_end_fastq_files2

    • Read_1_fastq

    • Read_2_fastq