QIIME 2 2026.10 is now available!

Hello QIIME 2 community and happy fall! :fallen_leaf: :jack_o_lantern:

We have another action-packed release for you with lots of exciting updates :chart_increasing: new features :tada: along with various maintenance work :hammer_and_wrench: and bug fixes :bug:

Like with each release, a huge thank you to everyone for their contributions this cycle! :hugs:

:police_car_light: Important Announcements :police_car_light:

Changes coming in 2027.1 :boom:

A few big changes will occur in the coming release cycle:

  • We will be removing the old QIIME 2 documentation (currently accessible at https://docs.qiime2.org/2024.10/) from https://docs.qiime2.org to make the new and improved documentation more apparent. It's come to our attention that Google still redirects to the old docs for a lot of QIIME 2 related queries. The old documentation will still be accessible directly in archive.org, and through a new Zenodo record that we will create to house them. Links to the old docs will break, but our hope is that this is net positive as it will ensure that users are getting to the newest content.
  • We are going to relax our constraint on informing the user community of breaking changes one release in advance. We will still do our best to minimize when these happen, but we think that in our attempt to provide a service to the user community (by keeping interfaces extremely stable) we're actually providing a disservice (by delaying changes that would improve the user experience). When breaking changes are made in a release, they will be announced in the release notes. We'll share some more details on our plan soon.

:bangbang: Breaking Changes :bangbang:

q2-cutadapt

  • The default value for the --p-times paramter in the qiime cutadapt trim-paired and qiime cutadapt trim-single will be removed. Currently, the default value (1) enforces trimming only one primer even if multiple primers are passed, which we believe is causing some confusion. Removing this default, will make this parameter required and ensure that everyone is aware of how many times primers will be trimmed from sequences.

RESCRIPt

  • @Vinzent_Risch and @SoilRotifer added deprecation notice on get_silva_data for --p-download-sequences; its functionality will be replaced with --p-seq-format.
  • @SoilRotifer renamed the get_silva_data param --p-include-species-labels to --p-include-organism-name-labels
    • The change in the parameter label is to make more explicit that the organism name is being used to fill in the "species" rank. The organism name is commonly defined by the researcher submitting the sequence, and often not curated. Also, SILVA does not curate down to the species rank. This option was intended for testing and curiosity purposes. We have added the explicit text in the action text: "NOT RECOMMENDED FOR GENERAL USE! CONSIDER FOR TESTING PURPOSES ONLY!". This echos the "Species-labels: caveat emptor!" warnings of the RESCRIPt SILVA tutorial.

Developer Announcements :brick:

Environment File Updates :open_file_folder:

  • 2026.10 is one of our bi-annual full releases, meaning we have updated various dependencies across our distribution environments. For a full list of dependencies that have changed, please see this announcement!

:sparkles: Here are the Highlights of the Release! :sparkles:

Q2View Updates :mag:

  • @Oddant1 fixed a visual bug causing the Visualization tab to appear before the viz was done parsing :bug:

Distribution Updates :package:

  • q2cli has been renamed to rachis-cli :seedling:
  • q2-fastp has been added to the qiime2 distribution :man_running::dashing_away:
  • q2-rgi has been added to the pathogenome distribution :microbe:

Docker Container Updates :jar:

  • The QIIME 2 Workshop Docker containers are now the default containers that are installed when following the instructions on the Library. If you haven't tried these containers out yet, we recommend it. The main difference is that they serve JupyterLab out of them and have QIIME 2 View built in, so they provide a very convenient way to interact with QIIME 2 for workshops and beyond. You can see a few screenshots of what this looks like as Figures 1 and 2 in the new and improved gut-to-soil tutorial.

Documentation Updates :book:

  • The gut-to-soil tutorial :poop: → :seedling: got a major overhaul! It now includes 21 figures that illustrate the data types used throughout a typical amplicon analysis workflow, it includes 17 Exercises and Solutions that guide readers through exploring the data, it integrates new analysis steps such as training a classifier on GTDB with RESCRIPt and q2-feature-classifier, it demonstrate new rachis functionality such as adding annotations to artifacts, and a lot more. This is now the main tutorial we recommend for getting started with QIIME 2, and it's workshop-ready designed to work smoothly with the QIIME 2 Workshop Docker containers. Enjoy!
  • There is improved documentation on using the CaptureHolder API to track automatic parameters in provenance.
  • rachis.org now has a proper homepage :house_with_garden:

Interface Updates :tv:

q2cli -> rachis-cli

  • We have renamed our command line interface as a part of our larger name change to rachis (formerly known as the QIIME 2 Framework aka Q2F). Overall this won't impact your experience as a user, but you will now see rachis-cli in place of q2cli within your newly installed environment(s) for 2026.10.
  • One new feature connected to this name change is the ability to use different command prefixes depending on the distribution you're using. The qiime2 distribution still supports usage of qiime <plugin> <action> and the moshpit distribution still supports mosh <plugin> <action>, but all distributions now support using rachis as the command prefix (i.e. rachis <plugin> <action>) as well.

Galaxy Releases :milky_way:

  • Some of you may have noticed our latest Galaxy release was 2026.1. This wasn't an unintentional lapse; we don't have the resources to maintain regular releases on Galaxy at this time, but this is something we hope to be able to pick back up in the future. We will keep you all updated if/when this does change!

Plugin Updates :electric_plug:

Changes in 2026.7.0 → 2026.10.0

q2-annotate

New and Improved! :rocket:

  • Add an action to transfer functional annotations (#349) (c9767e1 by ZuzanaSebb)
  • Add an action estimate-tfa to link taxonomy to per-contig features (#363) (635d2f9 by misialq)
  • Add an interactive TFA visualization (#364) (3bb2a3c by misialq)

q2-assembly

New and Improved! :rocket:

  • Allow prepending sample name when renaming contigs (#150) (910b796 by misialq)
  • Parallelize assemble-spades with Parsl (#170) (3c10451 by misialq)
  • Add explicit isolate mode to assemble-spades (#169) (09721e9 by misialq)
  • Filter contigs with on parameter, including sample or contig ids (#172) (1de8001 by ZuzanaSebb)

Bug Fixes :beetle:

  • Preserve suffix behavior in sort_alignment_maps (#174) (605284f by ebolyen)

Maintenance :gear:

  • Update the contig-consuming actions to align with the new file format (#171) (e9a333d by misialq)

q2-composition

New and Improved! :rocket:

Maintenance :gear:

q2-cutadapt

New and Improved! :rocket:

Bug Fixes :beetle:

  • Fix bugs related to uneven columns and invalid args in trim-metadata (#86) (ac415ae by Oddant1)

Maintenance :gear:

  • Add help text for metadata parameter in trim-single & trim-paired (#84) (7f6360e by colinvwood)

q2-fastp

New and Improved! :rocket:

q2-feature-classifier

Maintenance :gear:

  • Support filter_seqs changes in classify_hybrid_vsearch_sklearn (#225) (69d9193 by Macabe222)

q2-feature-table

New and Improved! :rocket:

New Features
Improvements
  • Allow FeatureData[LinkedSequence] as input to filter_seqs (#364) (a09c11b by Macabe222)
  • Allow FeatureData[LinkedSequence] as input to tabulate_seqs (#366) (0a97ceb by Macabe222)
  • Allow FeatureData[LinkedSequence] as input to merge_seqs (#365) (c91bff6 by Macabe222)
  • Refactor tabulate-seqs visualization (#369) (9c210db by Macabe222)

Bug Fixes :beetle:

  • Ensure tabulate-seqs shows every taxonomy in the collection and respects merge_method (#371) (db39e84 by gregcaporaso)

q2-mag

New and Improved! :rocket:

New Features
Improvements

Bug Fixes :beetle:

  • Do not use the _alignment suffix when filtering alignment maps (#23) (9f46d32 by misialq)
  • Preserve correct sample IDs while estimating abundance (#24) (66d362d by misialq)

q2-metadata

New and Improved! :rocket:

q2-taxa

New and Improved! :rocket:

Bug Fixes :beetle:

  • Support both include/exclude formats in filter_seqs and filter_table for backwards compatibility (#184) (0113eaf by lizgehret)

q2-types

New and Improved! :rocket:

Bug Fixes :beetle:

  • Add backwards compatible sample/suffix on BAM formats (#408) (0ebb43c by ebolyen)

q2-vizard

New and Improved! :rocket:

New Features
Improvements
  • Add colorBy support for numeric metadata cols (scatterplot) (#105) (d1dc4d3 by lizgehret)
  • Expose colorPalette parameter for all visualizers (#112) (61ec3ee by lizgehret)

Maintenance :gear:

q2templates

New and Improved! :rocket:

rachis-cli

Maintenance :gear:

rachis

New and Improved! :rocket:

Bug Fixes :beetle:

  • Make behavior of iter on ResultCollection match iter on the underlying dict (#974) (ed1c2d0 by Oddant1)

Maintenance :gear:

RESCRIPt

New and Improved! :rocket:

  • Add version 2.1 to get_eukaryome_data (#268) (5ad28a4 by mikerobeson)
  • Set validate_level to min in get-silva-data (#267) (6617b9b by VinzentRisch)
  • Add GenBank272_2026-06-07 & GenBank271_2026-04-07 to get_midori2_data (#269) (09f3a3e by mikerobeson)
  • Add support in get_silva_data for downloading aligned/unaligned SILVA files (#266) (af29a4f by mikerobeson)
  • Update get_gtdb_data url_type param to db_url and support newly available data servers (#271) (f7aa578 by mikerobeson)

Bug Fixes :beetle:

Share:
Back to Blog

Related Posts

View All Posts »