# QIIME 2 2025.4 is now available! **URL:** https://forum.qiime2.org/t/qiime-2-2025-4-is-now-available/33088 **Category:** Announcements **Tags:** release **Created:** [May 5, 2025, 7:09pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-is-now-available/33088 "2025-05-05T19:09:47Z") **Posts on this page:** 1 **Showing post:** 1
### Author: ![q2d2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/q2d2/32/613_2.png) [@q2d2](https://forum.qiime2.org/u/q2d2) #### Post date: [May 5, 2025, 7:09pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-is-now-available/33088/1 "2025-05-05T19:09:47Z")
## Hello QIIME 2 community! 👋🏼 We have a **BIG** release for you, almost in time for the end of April 2025! You can think of this is as our way of zero indexing the scheduled release date. 😉 There's a lot of new functionality and other improvements packed into this release, but we also have lots of big changes to our websites and documentation. This is all detailed below for your reading pleasure! You can also now find a [news page](https://qiime2.org/news/) (and a corresponding [RSS feed](https://qiime2.org/rss.xml)) where we plan to start sharing new content more regularly beginning this release cycle. We'll make an _Announcement_ on the QIIME 2 Forum when this goes live with additional details on how you can stay up-to-date. * * * ## 🚨 Important Announcements 🚨 ### `q2-vsearch` Software Bug in Prior Releases 🪲 **Affected Releases** The 2023.9, 2024.2, and 2024.5 shotgun/metagenome environments. **Description** A bug was discovered in the `vsearch` dependency of `q2-vsearch`. The bug manifests as possibly incorrect numbers of chimeric and non-chimeric sequence classifications from the `vsearch uchime-denovo` action. The magnitude of error is small--see [here](https://github.com/torognes/vsearch/issues/591) for more detailed information. ### ‼ Breaking Changes ‼ - [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt) - [q2-annotate](https://github.com/bokulich-lab/q2-annotate) (formerly q2-moshpit) * * * ## 2025.4 Release Highlights 🎇 **[qiime2.org](https://qiime2.org) Updates** 🏠 @ebolyen completely redesigned the QIIME 2 homepage - it was due for an update! Among the new features are a navigation bar that persists across the homepage, the (all new!) QIIME 2 Library, the Forum, and QIIME 2 View. We hope this will help you better discover and navigate all of the content and resources that we're building for the community. 🏙 * * * **[QIIME 2 Library](https://library.qiime2.org) Updates 📚** The [QIIME 2 Library](https://library.qiime2.org) has also been entirely remade and redesigned by @ebolyen! The QIIME 2 Library will now house installation instructions for the Distributions (see the [Quickstart](https://library.qiime2.org/quickstart) page) and [plugins](https://library.qiime2.org/plugins), [books and tutorials](https://library.qiime2.org/books), [videos](https://library.qiime2.org/videos), [workshop listings](https://library.qiime2.org/workshops), and [data resources](https://library.qiime2.org/data-resources) (such as taxonomy classifiers). The following plugins have been added to the library, in addition to plugins from the teams in the Caporaso and Bokulich labs: - [q2-metnet](https://library.qiime2.org/plugins/PlanesLab/q2-metnet) - [q2-micom](https://library.qiime2.org/plugins/micom-dev/q2-micom) - [q2-picrust](https://library.qiime2.org/plugins/picrust/q2-picrust2) - [q2-sourmash](https://library.qiime2.org/plugins/dib-lab/q2-sourmash) **Plugin developers** : learn how to add your plugins to the new library [here](https://develop.qiime2.org/en/latest/plugins/how-to-guides/distribute-on-library.html). [QIIME 2 Data Resources](https://library.qiime2.org/data-resources) are now accessible through the QIIME 2 Library. Additions in this cycle include: - @lizgehret added the 2024.09 Greengenes2 classifiers (thanks to @wasade and team for the new release!) 🦠 * * * **[QIIME 2 View](https://view.qiime2.org) Updates 🔍** - @Oddant1 added a new Metadata tab ([example](https://view.qiime2.org/metadata/?src=https://raw.githubusercontent.com/caporaso-lab/q2view-visualizations/main/uu-fasttree-empire.qzv)) to [QIIME 2 View](https://view.qiime2.org) that lists all of the Metadata contained within your provenance and provides information about why this metadata may be important. - @Oddant1 added the ability to search provenance for specific keys and (key, value) pairs on the provenance tab ([example](https://view.qiime2.org/provenance/?src=https://raw.githubusercontent.com/caporaso-lab/q2view-visualizations/main/uu-fasttree-empire.qzv)) of [QIIME 2 View](https://view.qiime2.org). This can help find Actions, Results, or other content in complex provenance graphs. - @Oddant1 adapted QIIME 2 View to make it easier to host from other locations (e.g., from a server behind your firewall, or out of a Docker container). `qiime tools view` now uses this on your machine, allowing you to interact with your visualizations offline exactly as you could through QIIME 2 View. See the q2cli section for more details. * * * **Documentation Updates** 📖 **Microbiome marker gene analysis with QIIME 2** : - @gregcaporaso led the transition from the "old docs" to the new QIIME 2 Amplicon Distribution documentation, now located at: [https://amplicon-docs.qiime2.org/](https://amplicon-docs.qiime2.org/). Changes made in this transition include: - Re-organization under the [Diataxis framework](https://diataxis.fr/) - Lots of content from the old docs was updated - The [Plugin Index](https://amplicon-docs.qiime2.org/en/latest/references/available-plugins.html) was completely rewritten, which can now be automatically generated for other plugins and distributions (example [here](https://library.qiime2.org/plugins/caporaso-lab/q2-boots/overview)) - An all new end-to-end analysis tutorial was added, the [Gut-to-Soil Microbiome Axis Tutorial](https://amplicon-docs.qiime2.org/en/latest/tutorials/gut-to-soil.html) **MOSHPIT tutorials:** - @misialq introduced many updates to the MOSHPIT (formerly QIIME 2 metagenome distribution) documentation, which is now available at [https://moshpit.qiime2.org](https://moshpit.qiime2.org). If you haven't started using the MOSHPIT Distribution for metagenomic analysis yet, we would love for you to try it out and provide any feedback that you might have! At this stage, we now have distribution-specific documentation that you can use to learn how to use the current distributions, including [_Microbiome marker gene analysis with QIIME 2_](https://amplicon-docs.qiime2.org/) and [_MOSHPIT tutorials_](https://moshpit.qiime2.org). Additionally, we have plugin-specific documentation for plugins that are not included in a distribution, including [genome-sampler](https://genome-sampler.readthedocs.io/en/latest/) and [q2-fmt](https://library.qiime2.org/plugins/qiime2/q2-fmt/tutorials). We have dataset focused tutorials that may ultimately cross distributions (e.g., to illustrate how to integrate metagenome and marker gene data), including the [gut-to-soil microbiome axis tutorial](https://gut-to-soil-tutorial.readthedocs.io/en/latest/). And finally, we have framework-level documentation for power users ([_Using QIIME 2_](https://use.qiime2.org)) and developers ([_Developing with QIIME 2_](https://develop.qiime2.org)). You can find all of this linked from the [_Books_ section of the QIIME 2 Library](https://library.qiime2.org/books). **TL;DR** : There are a lot of docs out there - if you're looking for something and can't find it, reach out to us on the Forum! 🤓 * * * **[Distribution Updates](https://github.com/qiime2/distributions)** 📦 - the MOSHPIT distribution got a significant upgrade: - q2-moshpit plugin was renamed to [q2-annotate](https://github/com/bokulich-lab/q2-annotate) to make a clear distinction between the plugin and the distribution itself - some actions and action inputs/outputs were renamed to ensure consistency across the distribution (please see "Plugin Updates" section below for details) - many new actions were added and the inputs to the existing actions were, in many cases, expanded by allowing additional input types - a new [tutorial page](https://moshpit.qiime2.org) was published * * * **[Framework Updates](https://github.com/qiime2/qiime2)** 🌳 - @lizgehret added support for semantic versioning of our [Archive Formats](https://develop.qiime2.org/en/latest/framework/references/archive-versions.html) (i.e., the format used to write `.qza` and `.qzv` files). 📑 Beginning with this release, our Archive Formats will now be versioned in `{major}.{minor}` format (e.g., `7.0`) where previous there was no minor version (e.g., `6`). This will allow us to make minor changes that are ensured to be backwards compatible within their major version (i.e. versions 7.0 -\> 7.n will all be backwards compatible within 7.\*, while versions 8.0+ won't be). - @lizgehret added the new v7.0 Archive Format 🖼. Additions in this new format include: * * * **Plugin Updates** 🔌 @lizgehret completed the following maintenance/modernization work for all plugins within QIIME 2 Distributions: - Transitioned all plugins' Python setup files from `setup.py` to `pyproject.toml` ⚙ This update simplifies and modernizes a plugin's setup, making it easier to read and maintain. - Replaced all uses of the deprecated `pkg_resources` package actions with the supported `importlib-*` equivalent actions. These updates align with the broader Python packaging ecosystem's push for modernization, ensuring compatibility with evolving tools and workflows 🛠 - [q2-annotate](https://github/com/bokulich-lab/q2-annotate) (formerly q2-moshpit) - [q2-assembly](https://github.com/bokulich-lab/q2-assembly) - [q2-composition](https://github.com/qiime2/q2-composition) - [q2-cutadapt](https://github.com/qiime2/q2-cutadapt) - [q2-feature-table](https://github.com/qiime2/q2-feature-table) - [q2-quality-control](https://github.com/qiime2/q2-quality-filter) - [q2-quality-filter](https://github.com/qiime2/q2-quality-filter) - [q2-types](https://github.com/qiime2/q2-types) - [q2-vizard](https://github.com/qiime2/q2-vizard) - [q2-vsearch](https://github.com/qiime2/q2-vsearch) - [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt) * * * **Docker Container Updates** 🫙 We now provide a Docker container that includes a Jupyter Lab server and some other niceties, which we use for teaching workshops. Learn how to use it to teach your own events [here](https://use.qiime2.org/en/latest/how-to-guides/use-the-workshop-container.html). * * * ## Coming up next! ➡ ### Interface Changes in QIIME 2 2025.10 💥 #### Plugin-Specific Changes 🔌 - [q2-quality-control](https://github.com/qiime2/q2-quality-control) - [q2-composition](https://github.com/qiime2/q2-composition) #### Distribution-Specific Changes 📦 - [MOSHPIT Distribution](https://moshpit.qiime2.org) - Plugins within the MOSHPIT Distribution (formerly the _Metagenome Distribution_) will have some interface changes throughout. - **NOTE** : While `moshpit` is still in beta release, you can expect some breaking changes between releases so we can quickly adapt to user needs. Be sure to check out the [moshpit pre-print](https://doi.org/10.1101/2025.01.27.635007) if you haven't already! #### Python Versioning Changes 🐍 - **Target for 2025.10:** Python 3.10 or 3.11, with a final decision posted on our mid-cycle dependency update announcement - **Target for 2026.4:** Python 3.12 * * * ## Thank you! 🙏🏻 As always, thanks to our _amazing_ community of developers, forum moderators, and users! We couldn't do it without you! If you're a QIIME 2 user and want to get more involved in the community, check out some content that @gregcaporaso put together on the topic in [_Using QIIME 2_](https://use.qiime2.org/en/latest/how-to-guides/get-involved.html). Have fun, and see you on the QIIME 2 Forum! 🧑‍💻🦠 --- _[View the full topic](https://forum.qiime2.org/t/qiime-2-2025-4-is-now-available/33088)._