Stable:
Devel:

MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.

MultiQC is written in Python (tested with v2.7 / v3.4 / v3.5) and is available on the Python Package Index.

Currently, supported tools include:

• Quality control & pre-processing
  • FastQC
  • FastQ Screen
  • Cutadapt
  • Skewer
• Read aligners
  • STAR
  • Tophat
  • Bowtie
  • Bowtie 2
  • Bismark
  • HiCUP
• Post-alignment tools
  • Subread featureCounts
  • Samblaster
  • Picard (MarkDuplicates, InsertSizeMetrics, GcBiasMetrics, HsMetrics, OxoGMetrics)
  • Preseq
  • Qualimap (BamQC, RNASeq)

More modules are being written all of the time. Please suggest any ideas as a new issue (include an example log file if possible).

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

Alternatively, you can install using Conda from the bioconda channel:

conda install -c bioconda multiqc

Once installed, you can use MultiQC by navigating to your analysis directory (or a parent directory) and running the tool:

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.html by default. Tab-delimited data files are also created in multiqc_data/, containing extra information. These can be easily inspected using Excel (use --data-format to get yaml or json instead).

For more detailed instructions, run multiqc -h or see the documentation.

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)

Many thanks to those who have helped out with with project.

• Project lead and main author: @ewels
• Early code refactoring help: @moonso
• Early version of Qualimap module: @guillermo-carrasco
• Skewer and Samblaster modules: @dakl
• Samtools stats module: @lpantano
• Tweaks / core help: @robinandeer and @avilella