Find documentation and example reports at multiqc.info
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MultiQC is written in Python (v2.7 / v3.4) and contains modules for a number of common tools. Currently, these include:
- Quality control & pre-processing
- Read aligners
- Post-alignment tools
More to come soon. Please suggest any ideas as a new issue (include an example log file if possible).
MultiQC comes with a graphical app for OS X. To use, download MultiQC.app.zip
from the releases page
and unzip the archive. Double click MultiQC.app to launch, then
drag your analysis directory onto the window.
The app can be run from anywhere, though we recommend copying to your Applications directory.
A similar graphical utility for Windows is planned for a future release.
You can install MultiQC from PyPI
using pip as follows:
pip install multiqc
If you would like the development version instead, the command is:
pip install git+https://github.com/ewels/MultiQC.git
Then it's just a case of going to your analysis directory and running the script:
multiqc .
That's it! MultiQC will scan the specified directory ('.' is the current dir) and produce a report detailing whatever it finds.
The report is created in multiqc_report/multiqc_report.html by default.
A zip file of the report is also generated to facilitate easy transfer and sharing.
Tab-delimited data files are also created in multiqc_report/report_data/,
containing extra information. These can be easily inspected using Excel.
For more detailed instructions, run multiqc -h
Contributions and suggestions for new features are welcome, as are bug reports! Please create a new issue for any of these, including example reports where possible.
Pull requests with new code are always gladly received, see the contributing notes for details. These notes include extensive help with how to use the built in code.
If in doubt, feel free to get in touch with the author: @ewels (phil.ewels@scilifelab.se)