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Aggregate results from bioinformatics analyses across many samples into a single report.

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Aggregate bioinformatics results across many samples into a single report.

Stable:
Devel:

MultiQC is written in Python (v2.7 / v3.4) and contains modules for a number of common tools. Currently, these include:

More to come soon. Please suggest any ideas as a new issue (include an example log file if possible).

Graphical Usage

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.

Command Line Usage

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 & Support

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)

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Aggregate results from bioinformatics analyses across many samples into a single report.

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