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FastQC Report Generator

FastQC Report Generator is a lightweight command-line tool for creating report files and visualisations from FastQC text files.

System Requirements

  • Python 3.4+ is required to run FastQC Report Generator.
  • FastQC Report Generator requires the following scientific libraries (which can be installed using pip or conda):
    • Matplotlib
    • Seaborn
    • NumPy
    • Pandas
    • SciPy

Installation

FastQC Report Generator does not require an installation procedure, simply open the terminal in Linux / MacOS or the Command Prompt in Windows, navigate to the fastqc_report directory and run fastqc_report.py (see below) using Python from the command-line.

Usage

To generate reports for specific FastQC modules (e.g., Per base sequence quality (module 2) and K-mer Content (module 12) parsed from an input file (fastqc.txt) in output directory (outdir), type the following in the command-line:

python fastqc_report.py fastqc.txt outdir m2 m12 m1

To generate reports and graphs for all modules, type:

python fastqc_report.py fastqc.txt outdir m1 -all

Alternatively, all reports can be generated in the Python console by typing:

runfile("fastqc_report.py", args="fastqc.txt outdir m1 -all")

For additional help, add the –h or --help flag:

python fastqc_report.py -h