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https://github.com/MultiQC/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.
https://github.com/MultiQC/MultiQC

analysis bioconda bioinformatics data-visualization multiqc pypi python quality-control reporting seqera vizualisation

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

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  MultiQC






### Aggregate bioinformatics results across many samples into a single report



##### Find [documentation](http://multiqc.info/docs) and [example reports](https://multiqc.info/example-reports/) at [http://multiqc.info](http://multiqc.info)



[![PyPI Version](https://img.shields.io/pypi/v/multiqc)](https://pypi.python.org/pypi/multiqc/)

[![Bioconda Version](https://img.shields.io/conda/v/bioconda/multiqc?label=bioconda)](https://bioconda.github.io/recipes/multiqc/README.html)

[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtw354-red.svg)](http://dx.doi.org/10.1093/bioinformatics/btw354)



---



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



Reports are generated by scanning given directories for recognised log files.

These are parsed and a single HTML report is generated summarising the statistics

for all logs found. MultiQC reports can describe multiple analysis steps and

large numbers of samples within a single plot, and multiple analysis tools making

it ideal for routine fast quality control.



A very large number of Bioinformatics tools are supported by MultiQC. Please see the MultiQC website for a [complete list](https://multiqc.info/modules/).

MultiQC can also easily parse data from custom scripts, if correctly formatted / configured - a feature called [Custom Content](https://multiqc.info/docs/custom_content/).



More modules are being written all the time. Please suggest any ideas as a new

[issue](https://github.com/MultiQC/MultiQC/issues) _(please include example log files)_.



## Installation



You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc/)

using `pip` as follows:



```bash

pip install multiqc

```



Alternatively, you can install using [Conda](http://anaconda.org/)

from [Bioconda](https://bioconda.github.io/) ([set up your channels](https://bioconda.github.io/#usage) first):



```bash

conda install multiqc

```



If you would like the development version from GitHub instead, you can install it with `pip`:



```bash

pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git

```



MultiQC is also available via Docker and Singularity images, Galaxy wrappers, and

many more software distribution systems.

See [the documentation](https://multiqc.info/docs/getting_started/installation/) for details.



## Usage



Once installed, you can use MultiQC by navigating to your analysis directory

(or a parent directory) and running the tool:



```bash

multiqc .

```



That's it! MultiQC will scan the specified directory (`.` is the current dir)

and produce a report detailing whatever it finds.



![`cd test-data/data/modules/fastqc/v0.10.1 && multiqc .`](https://github.com/MultiQC/MultiQC/raw/main/docs/images/screenshots/fastqc-run.svg)



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](http://multiqc.info/docs/#running-multiqc).



## Citation



Please consider citing MultiQC if you use it in your analysis.



> **MultiQC: Summarize analysis results for multiple tools and samples in a single report.** 
 _Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller_ 


> Bioinformatics (2016) 


> doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354) 


> PMID: [27312411](http://www.ncbi.nlm.nih.gov/pubmed/27312411)



```BibTeX

@article{doi:10.1093/bioinformatics/btw354,

 author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},

 title = {MultiQC: summarize analysis results for multiple tools and samples in a single report},

 journal = {Bioinformatics},

 volume = {32},

 number = {19},

 pages = {3047},

 year = {2016},

 doi = {10.1093/bioinformatics/btw354},

 URL = { + http://dx.doi.org/10.1093/bioinformatics/btw354},

 eprint = {/oup/backfile/Content_public/Journal/bioinformatics/32/19/10.1093_bioinformatics_btw354/3/btw354.pdf}

}

```



## Contributions & Support



Contributions and suggestions for new features are welcome, as are bug reports!

Please create a new [issue](https://github.com/MultiQC/MultiQC/issues) for any

of these, including example reports where possible.

Pull-requests for fixes and additions are very welcome.

Please see the [contributing notes](https://github.com/MultiQC/MultiQC/blob/main/.github/CONTRIBUTING.md) for more information about how the process works.



MultiQC has extensive [documentation](http://multiqc.info/docs/development/)

describing how to write new modules, plugins and templates.



If in doubt, feel free to get in touch with the author directly:

[@ewels](https://github.com/ewels) ([email protected])



### Contributors



MultiQC is developed and maintained by Phil Ewels ([@ewels](https://github.com/ewels)) at [Seqera Labs](https://seqera.io/).

It was originally written at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/), part of [SciLifeLab](https://www.scilifelab.se/) in Sweden.



A huge thank you to all code contributors - there are a lot of you!

See the [Contributors Graph](https://github.com/MultiQC/MultiQC/graphs/contributors) for details.



MultiQC is released under the GPL v3 or later licence.