{"repo":"MultiQC/MultiQC","free":true,"listed":false,"github":"https://github.com/MultiQC/MultiQC","clone":"git clone https://github.com/MultiQC/MultiQC.git","description":"Aggregate results from bioinformatics analyses across many samples into a single report.","language":"JavaScript","stars":1487,"topics":["analysis","bioconda","bioinformatics","data-visualization","multiqc","pypi","python","quality-control","reporting","seqera","vizualisation"],"license":"GPL-3.0","category":"bioinformatics_tool","readme_excerpt":"
\n\n \n \n \n\n
\n\n### Aggregate bioinformatics results across many samples into a single report\n\n##### Find [documentation](https://docs.seqera.io/multiqc) and [example reports](https://seqera.io/multiqc/#reports) at [https://seqera.io/multiqc/](https://seqera.io/multiqc/)\n\n[](https://pypi.python.org/pypi/multiqc/)\n[](https://bioconda.github.io/recipes/multiqc/README.html)\n[](http://dx.doi.org/10.1093/bioinformatics/btw354)\n\n---\n\nMultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.\n\nReports are generated by scanning given directories for recognised log files.\nThese are parsed and a single HTML report is generated summarising the statistics\nfor all logs found. MultiQC reports can describe multiple analysis steps and\nlarge numbers of samples within a single plot, and multiple analysis tools making\nit ideal for routine fast quality control.\n\nA very large number of Bioinformatics tools are supported by MultiQC. Please see the MultiQC website for a [complete list](https://docs.seqera.io/multiqc/modules/).\nMultiQC can also easily parse data from custom scripts, if correctly formatted / configured - a feature called [Custom Content](https://docs.seqera.io/multiqc/custom_content).\n\nMore modules are being written all the time. Please suggest any ideas as a new\n[issue](https://github.com/MultiQC/MultiQC/issues) _(please include example log files)_.\n\n## Installation\n\nYou can install MultiQC using [uv](https://docs.astral.sh/uv/) (no separate Python installation required):\n\n```bash\nuv tool install multiqc\n```\n\nAlternatively, install from [PyPI](https://pypi.python.org/pypi/multiqc/) using `pip`:\n\n```bash\npip install multiqc\n```\n\nOr install using [Conda](http://anaconda.org/)\nfrom [Bioconda](https://bioconda.github.io/) ([set up your channels](https://bioconda.github.io/#usage) first):\n\n```bash\nconda install multiqc\n```\n\nIf you would like the development version from GitHub instead, you can install it with `uv` or `pip`:\n\n```bash\nuv tool install git+https://github.com/MultiQC/MultiQC.git\n```\n\n```bash\npip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git\n```\n\nMultiQC is also available via Docker and Singularity images, Galaxy wrappers, and\nmany more distribution methods.\nSee [the documentation](https://docs.seqera.io/multiqc/getting_started/installation/) for details.\n\n## Usage\n\nOnce installed, you can use MultiQC by navigating to your analysis directory\n(or a parent directory) and running the tool:\n\n```bash\nmultiqc .\n```\n\nThat's it! MultiQC will scan the specified directory (`.` is the current dir)\nand produce a report detailing whatever it finds.\n\n\n\n\n\nThe report is created in `multiqc_report.html` by default. Tab-delimited data\nfiles are also created in `multiqc_data/`, containing extra information.\nThese can be easily inspected using Excel (use `--data-format` to get `yaml`\nor `json` instead).\n\nFor more detailed instructions, run `multiqc -h` or see the\n[documentation](https://docs.seqera.io/multiqc/getting_started/running_multiqc).\n\n## Configuration\n\nTo customise your reports, MultiQC reads from a YAML config file. See the [configuration docs](https://docs.seqera.io/multiqc/getting_started/config) for the full list of options and search paths.\n\nYou can build a config file visually in your browser with the [MultiQC Configuration Wizard](https://seqera.io/multiqc_config_wizard). It has every option as a form field, with live YAML editor and schema validation as you type.\n\n## Citation\n\nPlease consider citing MultiQC if you use it in your analysis.\n\n> **MultiQC: Summarize analysis results for multiple tools and samples in a single report.** _Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller_ \n> Bioinformatics (2016) \n> doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354) \n> PMID: [27312411](http://www.ncbi.nlm.nih.gov/pubmed/27312411)\n\n```BibTeX\n@article{doi:10.1093/bioinformatics/btw354,\n author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},\n title = {MultiQC: summarize analysis results for multiple tools and samples in a single report},\n journal = {Bioinformatics},\n volume = {32},\n number = {19},\n pages = {3047},\n year = {2016},\n doi = {10.1093/bioinformatics/btw354},\n URL = { + http://dx.doi.org/10.1093/bioinformatics/btw354},\n eprint = {/oup/backfile/Content_public/Journal/bioinformatics/32/19/10.1093_bioinformatics_btw354/3/btw354.pdf}\n}\n```\n\n## Contributions & Support\n\nContributions and suggestions for new features are welcome, as are bug reports!\nPlease create a new [issue](https://github.com/MultiQC/MultiQC/issues) for any\nof these, including example reports where possible.\nPull-requests for fixes and additions are very welcome.\nPlease see the [contributing notes](https://github.com/MultiQC/MultiQC/blob/main/.github/CONTRIBUTING.md) for more information about how the process works.\n\nMultiQC has extensive [documentation](https://docs.seqera.io/multiqc/development)\ndescribing how to write new modules, plugins and templates.\n\nIf in doubt, feel free to get in touch with the author directly:\n[@ewels](https://github.com/ewels) (phil.ewels@seqera.io)\n\n### Contributors\n\nMultiQC is developed and maintained by Phil Ewels ([@ewels](https://github.com/ewels)) at [Seqera Labs](https://seqera.io/).\nIt was originally written at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/), part of [SciLifeLab](https://www.scilifelab.se/) in Sweden.\n\nA huge thank you to all code contributors - there are a lot of you!\nSee the [Contributors Graph](https://github.com/MultiQC/MultiQC/graphs/contributors) for details.\n\nMultiQC is released under the GPL v3 or later 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