README.md
1# 
2
3### Aggregate bioinformatics results across many samples into a single report
4
5##### Find [documentation](http://multiqc.info/docs) and [example reports](http://multiqc.info/examples/rna-seq/multiqc_report.html) at [http://multiqc.info](http://multiqc.info)
6
7[](https://pypi.python.org/pypi/multiqc/)
8[](https://anaconda.org/bioconda/multiqc)
9[](https://hub.docker.com/r/ewels/multiqc/)
10[](https://github.com/ewels/MultiQC/actions?query=workflow%3A%22MultiQC+-+Linux%22)
11[](https://github.com/ewels/MultiQC/actions?query=workflow%3A%22MultiQC+-+Windows%22)
12
13[](https://gitter.im/ewels/MultiQC)
14[](http://dx.doi.org/10.1093/bioinformatics/btw354)
15
16---
17
18MultiQC is a tool to create a single report with interactive plots
19for multiple bioinformatics analyses across many samples.
20
21MultiQC is written in Python (tested with v3.6+). It is
22available on the [Python Package Index](https://pypi.python.org/pypi/multiqc/)
23and through conda using [Bioconda](http://bioconda.github.io/).
24
25Reports are generated by scanning given directories for recognised log files.
26These are parsed and a single HTML report is generated summarising the statistics
27for all logs found. MultiQC reports can describe multiple analysis steps and
28large numbers of samples within a single plot, and multiple analysis tools making
29it ideal for routine fast quality control.
30
31There a very large number of Bioinformatics tools supported by MultiQC.
32Please see the MultiQC website for a [complete list](https://multiqc.info/#supported-tools).
33
34MultiQC can also easily parse data from custom scripts, if correctly formatted / configured.
35See the [MultiQC documentation](http://multiqc.info/docs/#custom-content) for more information.
36
37Please note that some modules only recognise output from certain tool subcommands.
38Please see the [module documentation](http://multiqc.info/docs/#multiqc-modules) for more information.
39
40More modules are being written all of the time. Please suggest any ideas as a new
41[issue](https://github.com/ewels/MultiQC/issues) _(include an example log file if possible)_.
42
43## Installation
44
45You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc/)
46using `pip` as follows:
47
48```bash
49pip install multiqc
50```
51
52Alternatively, you can install using [Conda](http://anaconda.org/)
53from the [bioconda channel](https://bioconda.github.io/):
54
55```bash
56conda install -c bioconda multiqc
57```
58
59If you would like the development version instead, the command is:
60
61```bash
62pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git
63```
64
65MultiQC is also available in the
66[Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/view/engineson/multiqc/).
67
68## Usage
69
70Once installed, you can use MultiQC by navigating to your analysis directory
71(or a parent directory) and running the tool:
72
73```bash
74multiqc .
75```
76
77That's it! MultiQC will scan the specified directory (`.` is the current dir)
78and produce a report detailing whatever it finds.
79
80The report is created in `multiqc_report.html` by default. Tab-delimited data
81files are also created in `multiqc_data/`, containing extra information.
82These can be easily inspected using Excel (use `--data-format` to get `yaml`
83or `json` instead).
84
85For more detailed instructions, run `multiqc -h` or see the
86[documentation](http://multiqc.info/docs/#running-multiqc).
87
88## Development
89
90MultiQC has been written in a way to make extension and customisation as easy as possible.
91The documentation has a large section describing how to [code with MultiQC](https://multiqc.info/docs/#coding-with-multiqc) and you can find an example plugin at [https://github.com/MultiQC/example-plugin](https://github.com/MultiQC/example-plugin).
92
93Pull-requests for fixes and additions are very welcome.
94Please see the [contributing notes](https://github.com/ewels/MultiQC/blob/master/.github/CONTRIBUTING.md) for more information about how the process works.
95
96## Citation
97
98Please consider citing MultiQC if you use it in your analysis.
99
100> **MultiQC: Summarize analysis results for multiple tools and samples in a single report.** <br> _Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller_ <br>
101> Bioinformatics (2016) <br>
102> doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354) <br>
103> PMID: [27312411](http://www.ncbi.nlm.nih.gov/pubmed/27312411)
104
105```BibTeX
106@article{doi:10.1093/bioinformatics/btw354,
107 author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},
108 title = {MultiQC: summarize analysis results for multiple tools and samples in a single report},
109 journal = {Bioinformatics},
110 volume = {32},
111 number = {19},
112 pages = {3047},
113 year = {2016},
114 doi = {10.1093/bioinformatics/btw354},
115 URL = { + http://dx.doi.org/10.1093/bioinformatics/btw354},
116 eprint = {/oup/backfile/Content_public/Journal/bioinformatics/32/19/10.1093_bioinformatics_btw354/3/btw354.pdf}
117}
118```
119
120## Contributions & Support
121
122Contributions and suggestions for new features are welcome, as are bug reports!
123Please create a new [issue](https://github.com/ewels/MultiQC/issues) for any
124of these, including example reports where possible. MultiQC has extensive
125[documentation](http://multiqc.info/docs) describing how to write new modules,
126plugins and templates.
127
128There is a chat room for the package hosted on Gitter where you can discuss
129things with the package author and other developers:
130<https://gitter.im/ewels/MultiQC>
131
132If in doubt, feel free to get in touch with the author directly:
133[@ewels](https://github.com/ewels) (phil.ewels@scilifelab.se)
134
135### Contributors
136
137Project lead and main author: [@ewels](https://github.com/ewels)
138
139There are a lot of other code contributors though!
140See the [Contributors Graph](https://github.com/ewels/MultiQC/graphs/contributors) for details.
141
142MultiQC is released under the GPL v3 or later licence.
143
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