[Preview] QIIME 2 2025.4 development changelog

Developer Discussion
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:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2025.4

This post is a live-document which will be updated throughout our development cycle. Any links will in this topic will be broken until the release is officially published. When we are ready for release, we’ll copy this changelog and create a new post in the Announcements category.

Developer Project Board:

QIIME 2 2025.4 Project on Github

:rotating_light: Important Announcements :rotating_light:

Interface Changes coming in QIIME 2 2025.10 :boom:

Python Versioning :snake:

  • Target for 2025.10: Python
  • Target for 2026.4: Python

:bangbang: Breaking Changes :bangbang:

Here are the highlights of the release! :sparkler:

qiime2.org updates :house:

QIIME 2 View Updates :mag:

QIIME 2 Library Updates :books:

QIIME 2 Forum Updates :page_facing_up:

Distribution Updates :package:

Framework Updates :deciduous_tree:

Interface Updates :tv:

Plugin Updates :electric_plug:

  • q2-quality-filter

    • The q-score action now processes and returns paired end reads.

  • q2-composition

    • @salias made an improvement to da-barplot such that consistent coloring is used for enriched and depleted features, regardless of whether any enriched features are presented. The colors used here are blue (for enriched features) and orange (for depleted features). Previously, if no features were enriched, depleted features would be presented in blue. This is inconvenient when comparing these plots side-by-side.

  • q2-cutadapt

    • Parameters that allow unconditional removal of bases from the beginning and ends of reads were added to the trim-single and trim-paired actions.

Community Plugin Updates :electric_plug:

Documentation Updates :open_book:

Docker Container Updates :jar: