{"id":13703782,"url":"https://github.com/MultiQC/MultiQC","last_synced_at":"2025-05-05T07:31:50.791Z","repository":{"id":35900703,"uuid":"40187375","full_name":"MultiQC/MultiQC","owner":"MultiQC","description":"Aggregate results from bioinformatics analyses across many samples into a single report.","archived":false,"fork":false,"pushed_at":"2025-04-30T18:52:27.000Z","size":43724,"stargazers_count":1293,"open_issues_count":229,"forks_count":616,"subscribers_count":33,"default_branch":"main","last_synced_at":"2025-04-30T19:23:20.045Z","etag":null,"topics":["analysis","bioconda","bioinformatics","data-visualization","multiqc","pypi","python","quality-control","reporting","seqera","vizualisation"],"latest_commit_sha":null,"homepage":"https://seqera.io/multiqc/","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MultiQC.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2015-08-04T13:47:05.000Z","updated_at":"2025-04-30T18:03:00.000Z","dependencies_parsed_at":"2023-09-22T02:52:21.347Z","dependency_job_id":"344895b5-22eb-4620-a56e-33acdde95a25","html_url":"https://github.com/MultiQC/MultiQC","commit_stats":{"total_commits":4984,"total_committers":249,"mean_commits":"20.016064257028113","dds":0.5449438202247191,"last_synced_commit":"ffbeb704e24063ff0f0930a27bc0b05b03e487e8"},"previous_names":["multiqc/multiqc","ewels/multiqc"],"tags_count":48,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MultiQC%2FMultiQC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MultiQC%2FMultiQC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MultiQC%2FMultiQC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MultiQC%2FMultiQC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MultiQC","download_url":"https://codeload.github.com/MultiQC/MultiQC/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252458481,"owners_count":21751046,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["analysis","bioconda","bioinformatics","data-visualization","multiqc","pypi","python","quality-control","reporting","seqera","vizualisation"],"created_at":"2024-08-02T21:01:00.100Z","updated_at":"2025-05-05T07:31:45.784Z","avatar_url":"https://github.com/MultiQC.png","language":"JavaScript","readme":"\u003ch1\u003e\n\u003cpicture\u003e\n  \u003csource media=\"(prefers-color-scheme: dark)\" srcset=\"https://github.com/MultiQC/MultiQC/raw/main/docs/images/MultiQC_logo_darkbg.png\"\u003e\n  \u003csource media=\"(prefers-color-scheme: light)\" srcset=\"https://github.com/MultiQC/MultiQC/raw/main/docs/images/MultiQC_logo.png\"\u003e\n  \u003cimg src=\"https://github.com/MultiQC/MultiQC/raw/main/docs/images/MultiQC_logo.png\" alt=\"MultiQC\"\u003e\n\u003c/picture\u003e\n\u003c/h1\u003e\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://multiqc.info/example-reports/) at [http://multiqc.info](http://multiqc.info)\n\n[![PyPI Version](https://img.shields.io/pypi/v/multiqc)](https://pypi.python.org/pypi/multiqc/)\n[![Bioconda Version](https://img.shields.io/conda/v/bioconda/multiqc?label=bioconda)](https://bioconda.github.io/recipes/multiqc/README.html)\n[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtw354-red.svg)](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 from [PyPI](https://pypi.python.org/pypi/multiqc/)\nusing `pip` as follows:\n\n```bash\npip install multiqc\n```\n\nAlternatively, you can 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 `pip`:\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 software distribution systems.\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\u003c!-- RICH-CODEX fake_command: \"multiqc .\" --\u003e\n\n![`cd test-data/data/modules/fastqc/v0.10.1 \u0026\u0026 multiqc .`](https://github.com/MultiQC/MultiQC/raw/main/docs/images/screenshots/fastqc-run.svg)\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## Citation\n\nPlease consider citing MultiQC if you use it in your analysis.\n\n\u003e **MultiQC: Summarize analysis results for multiple tools and samples in a single report.** \u003cbr\u003e _Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller_ \u003cbr\u003e\n\u003e Bioinformatics (2016) \u003cbr\u003e\n\u003e doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354) \u003cbr\u003e\n\u003e 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 \u0026 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 licence.\n","funding_links":[],"categories":["Next Generation Sequencing","Ranked by starred repositories"],"sub_categories":["Sequence Processing"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FMultiQC%2FMultiQC","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FMultiQC%2FMultiQC","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FMultiQC%2FMultiQC/lists"}