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