MultiQC

YouTube video by Nextflow Phil Ewels: MultiQC: New features and flexible data parsing

That and more! Custom Python scripts work too, you might like this quick recap of new features from in a short talk from 2024: youtu.be/-qwmeHyY6T0?...

🎉Celebrating 10 Years of @multiqc.info

What began as a simple QC reporting tool has evolved into an essential resource used by thousands worldwide, becoming integral to the #bioinformatics ecosystm.

🔍 Discover MultiQC: hubs.la/Q03Bh0wM0

I'm incredibly grateful for the amazing community that's contributed, provided feedback, and helped shape it into what it is today. This journey wouldn't have happened without you all, a testament to the power of #openscience

Here's to the next decade of making #bioinformatics QC beautiful! 🧬

🎉 Today marks 10 years since the very first @multiqc.info commit!

What started as a simple tool for QC reports has grown into something used by thousands of labs worldwide. It's become a foundational tool in the fabric of #bioinformatics and it's a joy to see it play a small part in global research

Seqera Seqera | The Home for Open Science | From the creators of Nextflow, Wave, and MultiQC

9/
Tools you need:
FastQC: first defense

MultiQC: overview across samples

IGV: visualize coverage & peaks

PCA plots: always

Links:
www.bioinformatics.babraham.ac.uk/projects/fa...
multiqc.info/
software.broadinstitute.org/software/igv/

Release v1.28 · MultiQC/MultiQC MultiQC v1.28 - 2025-03-21 JSON schema for MultiQC config & AI summaries fixes and optimizations. Feature updates and improvements Add JSON schema for config (#3100) Allow configure dynamic toolbo...

Modules #QUAST and #Trimmomatic got minor updates, and #VEP and #BclConvert got bugfixes. There were also a number of tweaks and fixes for AI summaries ✨

See the full changelog here: github.com/MultiQC/Mult...

Configuration | Seqera Docs Settings to tweak how MultiQC works

Ever wanted to set report Toolbox settings from the CLI whilst generating reports? (highlight, hide, and rename samples) Now you can! We finally closed this ancient issue from 2016 🧓🏻🌈🎉 github.com/MultiQC/Mult...

See the docs to get started: docs.seqera.io/multiqc/gett...

Another quality of life improvement is that we now have a #JSONschema via @pydantic.dev for #MultiQC configuration files 🎉

This has been added to schemastore.org so that config files in #VSCode & other IDEs automatically get integrated error checking as you type, see docs.seqera.io/multiqc/gett...

a man in a red sweater is dancing in a living room in front of a fireplace . ALT: a man in a red sweater is dancing in a living room in front of a fireplace .

Did you see, #MultiQC v1.28 went out a few days ago!

There are a handful of release highlights for this version, but perhaps the most exciting is that .gif, .webp and .tiff files are now supported for #CustomContent - you can finally put your favourite gifs into reports! Just name them *_mqc.gif

Seqera Seqera | The Home for Open Science | From the creators of Nextflow, Wave, and MultiQC

🔗 QC reads with FastQC: www.bioinformatics.babraham.ac.uk/projects/fa...
RNAseqqc github.com/getzlab/rna...
🔗 Check out multiQC for aggregated reports:multiqc.info/ multiqc.info/🔬 Learn to visualize data with IGV: software.broadinstitute.org/software/igv/

Start every analysis with rigorous QC! 🚀

MultiQC | Seqera Aggregate results from bioinformatics analyses across many samples into a single report

One of my top tools for primary data quality analysis, so essential for downstream analyses: #MultiQC. This recent update is incredibly useful!

seqera.io/multiqc/

github.com/MultiQC/Mult...

Multiqc, a rose emoji and the version (1.27.1)

Roses are red,
Violets are blue,
@multiqc.info knows it's Valentine too

AI Summaries now available in MultiQC | Seqera AI Summaries allow MultiQC users to quickly generate summaries of their reports, offering insights without needing to comb through every detail manually.

Read the blog post: hubs.la/Q033Kjp30

The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉

Find out more: hubs.la/Q033Kjp30

One of the cooler things I saw at the Nextflow summit a few months ago. Can't wait to try this.

AI summaries | Seqera Docs Using AI to summarise MultiQC reports

We're really excited to hear what folks make of the new functionality. Give it a try now with v1.27 and check out the documentation at docs.seqera.io/multiqc/ai

github.com/MultiQC/Mult...

AI Summaries now available in MultiQC | Seqera AI Summaries allow MultiQC users to quickly generate summaries of their reports, offering insights without needing to comb through every detail manually.

We made this functionality as flexible as possible. It works out of the box with @seqera.io AI and also #OpenAI and #AnthropicAI.

Reports also have "Copy prompt" options to paste into whatever LLM you like.

Read more in the blog post: hubs.ly/Q033KvM10

The premise is fairly simple: #MultiQC can now build prompts including sample data and send these to LLM services to get summaries.

This can be done at report-generation time, with the summary is part of the HTML. But also *interactively* on-demand when reading the report.

MultiQC v1.27 was released yesterday. It includes one major new feature:

=== ✨ AI summaries ✨ ===

LLMs are a natural next step for helping scientists understand large datasets. @multiqc.info now has built-in integration with @seqera.io AI as well as #OpenAI and #AnthropicAI 🤖

I'm excited to see my contributions made it into this version! It was a lot easier to add new modules than I expected. If anyone is wishing a tool was supported, you should just try adding it.

Super cool! MultiQC now supports Haplocheck! 🚀 @sebschoenherr.bsky.social @whansi.bsky.social

Nice tiny Xmas gift in the new release 🎄. Percolator feature weights can be simply plotted now with multiQC!

Release v1.26 · MultiQC/MultiQC MultiQC v1.26 - 2024-12-17 Christmas release! 10 new modules, 11 improved modules, and a few core improvements. Highlights Custom content: allow quoting strings in CSV to prevent interpreting them...

And finally a bunch of core improvements! #Python 3.13 now officially supported, and 3.8 dropped. Tooltips, improved memory efficiency, properly sorted samples and strings, default settings for @cursor_ai editor and more!

github.com/MultiQC/Mult...

💫 12 modules updated with features, tweaks and fixes:

- GATK BQSR
- Pychopper
- fastp
- RNA-SeqC
- phantompeakqualtools
- QualiMap RNASeq
- QualiMap BamQC
- DRAGEN
- Interop
- Dedup
- Bclconvert
- Nanostat

🆕 10 new modules supporting new tools in this release:

- MosaiCatcher
- ataqv
- telseq
- Cell
- GTDB
- Checkm
- Checkm2
- Haplocheck
- mgikit
- Percolator

New in this release: report toolbox settings (highlights, renaming, hiding samples) are automatically saved to the browser's local storage. So next time you open the same report they'll show up again! ✨💾

Sneaking a little holiday gift in at the last moment: @multiqc.info v1.26 just released!

- 🆕 10 new tools supported
- 💫 12 modules updated
- 🛠️ Bug fixes, improvements and refactoring!

If you're quick, you might see a little christmassy easter egg!

github.com/MultiQC/Mult...

I'm looking for a nice pull-quote about @multiqc.info that we can use in some @seqera.io materials, if anyone fancies dropping something nice into the comments as an early Christmas present for me, that would be much appreciated! 🙏🏻 😅

Sequence analysis / Quality Control / Hands-on: Quality Control Analyses of sequences

🍎 Master the art of Quality Control for NGS data with @galaxytraining.bsky.social! Learn how to assess, improve, and summarize sequencing quality using tools like FASTQC, Cutadapt, and MultiQC.
Catch errors early and save time on downstream analysis!

training.galaxyproject.org/training-mat...

Example of YAML config with environment variable string interpolation.

A highlight of this release is improved config parsing, with better support for environment variables 💫

Every MultiQC config option can now be set via an env var, and YAML configs can interpolate env vars into their strings: