iiinova — where your digital self keeps evolving

🐛 Fixes for Bcftools, Cell Ranger ARC, Dragen FastQC, Haplocheck, a race producing empty plot zip exports, and env vars being stored as strings rather than their actual types. 🔧 Minimum Python is now 3.9, and Polars got reworked (including a Pyodide-compatible build for in-browser use).

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🛠 Bigger module updates for Bases2Fastq (major overhaul), Falco (now auto-detected), Fastp (% surviving bases), and Sequali (expanded stats + normalised plots). ✨ Plus section alerts for filtered samples, per-tab plot configs, custom favicons, and a defaultsort fix for the first table column.

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Also in v1.35: eight new modules 🧩 CheckAtlas (single-cell atlas QC), Deacon (host depletion), FastQE (FASTQ quality as emoji 🤓), hicstuff (Hi-C contact maps), HiFi-Trimmer (PacBio HiFi adapters), Riker (Rust port of Picard QC), sincei (single-cell epigenomics), and native Trim Galore v2!

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MultiQC Configuration Reference | Seqera Docs

The @pydantic.dev model that powers the config is also used to autogenerate comprehensive new documentation, and a JSON schema that goes to schemastore.org - this means if you save a 'multiqc_config.yaml' file in #VSCode you'll get native inline validation 🚀 docs.seqera.io/multiqc/conf...

docs.seqera.io

This document describes all configuration options available in MultiQC.

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MultiQC Configuration Wizard

The Config Wizard is a static HTML page that ships with MultiQC, but easiest to try online (works entirely in your browser, no network traffic): 👉 seqera.io/multiqc_conf...

seqera.io

Build a multiqc_config.yaml visually. Live YAML editor, schema validation, inline error markers, dark mode. In your browser.

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Seqera @seqera.io · 06/01/2026

Happy to say MultiQC v1.35 is out 🎉 The headline feature: a MultiQC Config Wizard 🧙‍♂️ Browse every config option with help text and examples, fill out a form with live validation, or paste in your existing YAML and have it explained and checked. Video below 👇

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New year, new opportunities!🎆 Subscribe to our monthly newsletter for exclusive @nextflow.io and Seqera updates, including new product features, training sessions, events, and more. 📧 hubs.la/Q03YRwmn0

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Maxime U Garcia @maxulysse.github.io · 19/12/2025

On a server bright on Christmas night, MultiQC sang, “All stats unite!” From FastQC, pipelines adored, One tidy report—what could you want more?

First line Multiqc CLI output, saying MultiQC, followed by a Xmas tree emoji and version 1.31

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Release v1.33 · MultiQC/MultiQC

Install or upgrade now: pip install multiqc --upgrade Full changelog and release notes: github.com/MultiQC/MultiQC/releases/tag/v1.33 Huge thanks to everyone who contributed to this release! 🙏

github.com

New modules Seqkit stats (#3401) A cross-platform and ultrafast toolkit for FASTA/Q file manipulation RiboTish (#3384) Ribo-seq quality metrics Sylph (#3370) Sylph is a program that perform...

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Bug fixes 🐛 • FastQC heatmap Plotly export fixed • Sample filter buttons now work correctly • Homer unique/total count swap corrected • Samtools coverage no longer crashes on files with incorrect column counts • Bar graph reference lines now work when horizontal • Lima delimiter parsing fixed

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Module updates 🔧 • fastp can now name samples using --report_title from the command • Version fetching added for HiCUP, QoRTs, QualiMap, and RNA-SeQC • BISCUIT module refactored for better consistency with the rest of the codebase • Glimpse now shows more decimal precision in general stats table

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Features and improvements ✨ • Sample groups configuration for visual grouping in bar graphs • Custom logos now support dark mode and custom widths • Configurable help text for General Stats • Axis options for applying log scales to specific axes • Custom content strips whitespace around categories

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New modules 📦 • Seqkit stats: ultrafast FASTA/Q file manipulation toolkit • RiboTish: Ribo-seq quality metrics for ribosome profiling • Sylph: metagenomic profiling and containment ANI querying for shotgun sequencing • BBsplit: new submodule for the BBtools suite

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MultiQC v1.33 is out! 🎉 4 new modules, 60% faster parquet merging, and lots of improvements across the board. Here's what's new 🧵

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Seqera @seqera.io · 08/12/2025

Stay in the loop with everything @nextflow.io, @seqera.io, @multiqc.info, and more!✉️ Subscribe to our newsletter to get monthly updates on new product features, industry and community insights, events, and training workshops. 📚 Subscribe now: hubs.la/Q03Xf2NB0

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Seqera @seqera.io · 04/12/2025

Importance of being open!🌍 One of the greatest strengths of @multiqc.info is open source development.🧵What started as a one-person project in 2015 has grown into a collaborative effort involving 235 contributors today.🧵 📚 Read the blog post: hubs.la/Q03WRgb20

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MultiQC @multiqc.info · 26/11/2025

#NextflowSummit now available on-demand! Be sure to check out the "MultiQC turns 10" talk by @ewels.bsky.social 👀

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MultiQC @multiqc.info · 19/11/2025

💡A simple idea emerged from the frustration of manually parsing countless bioinformatics tool outputs.📊 That idea became MultiQC, and today we're celebrating 10 years of transforming global bioinformatics🌎 📗Read the highlights blog by @seqera.io: hubs.la/Q03TXC_N0

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Seqera @seqera.io · 24/10/2025

🎉 Celebrating 10 years of @multiqc.info! 📊 The numbers speak volumes: 🔹 Support for ~170 bioinformatics tools 🔹 1 run every 3 seconds (25k+ daily runs) 🔹 From single contributor to 235 contributors 🔹 7000+ journal citations (~8-9 per day) 📚 Discover a timeline of innovation: hubs.ly/Q03PsbTP0

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MultiQC @multiqc.info · 05/08/2025

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?...

youtu.be

Phil Ewels: MultiQC: New features and flexible data parsing

YouTube video by Nextflow

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Seqera @seqera.io · 05/08/2025

🎉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

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MultiQC @multiqc.info · 04/08/2025

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! 🧬

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MultiQC @multiqc.info · 04/08/2025

🎉 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

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Ming Tommy Tang @tommytang.bsky.social · 30/06/2025

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/

multiqc.info

Seqera

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

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MultiQC @multiqc.info · 09/04/2025

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...

docs.seqera.io

Configuration | Seqera Docs

Settings to tweak how MultiQC works

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MultiQC @multiqc.info · 09/04/2025

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...

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MultiQC @multiqc.info · 09/04/2025

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

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Ming Tommy Tang @tommytang.bsky.social · 25/01/2025

🔗 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.info

Seqera

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

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Miss Salmonella @misssalmonella.bsky.social · 28/01/2025

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...

seqera.io

MultiQC | Seqera

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

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Maxime U Garcia @maxulysse.github.io · 14/02/2025

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

Multiqc, a rose emoji and the version (1.27.1)

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Seqera @seqera.io · 23/01/2025

The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉 Find out more: hubs.la/Q033Kjp30

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Stephen Turner @stephenturner.us · 23/01/2025

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

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AI summaries | Seqera Docs

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...

docs.seqera.io

Using AI to summarise MultiQC reports

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AI Summaries now available in MultiQC | Seqera

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

hubs.ly

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

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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.

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Greg Fedewa @science.ninja · 23/12/2024

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 🤖

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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.

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Lukas Forer @lukfor.bsky.social · 22/12/2024

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

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jonasscheid.bsky.social @jonasscheid.bsky.social · 22/12/2024

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

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Release v1.26 · MultiQC/MultiQC

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...

github.com

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...

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💫 12 modules updated with features, tweaks and fixes: - GATK BQSR - Pychopper - fastp - RNA-SeqC - phantompeakqualtools - QualiMap RNASeq - QualiMap BamQC - DRAGEN - Interop - Dedup - Bclconvert - Nanostat

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🆕 10 new modules supporting new tools in this release: - MosaiCatcher - ataqv - telseq - Cell - GTDB - Checkm - Checkm2 - Haplocheck - mgikit - Percolator

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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! ✨💾

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