QIIME 2 2023.2 is now available!

The QIIME 2 2023.2 release is now available! Thanks to everyone involved for their hard work!

As a reminder, our next planned QIIME 2 release is scheduled for May 2023 (QIIME 2 2023.5), but please stay tuned for updates.

Check out the QIIME 2 2023.2 docs for details on installing the latest QIIME 2 release, as well as tutorials and other resources. Get in touch on the QIIME 2 Forum if you run into any issues!

Docker images have been built and are ready for use!

Here are the highlights of the release:

• q2-composition

  • @lizgehret fixed a in ANCOM-BC where a reference_level value was chosen that is a column within the metadata, but the associated IDs from that group are not found in the feature table No error would be raised, ANCOM-BC just defaulted back to alphabetical order for the intercept column
    This will now produce an error that includes the reference_level value, along with the IDs not found in the table
  • @lizgehret added type enforcement for the reference_level parameter, which now only allows numerical metadata columns to be used
  • @lizgehret added citations for ANCOM and ANCOM-BC methods
  • @lizgehret made some improvements to the tabulate visualizer:
    • Each tab now contains the data slice name and short descriptions for LFC and W-Scores
    • Columns used to calculate the intercept are included at the top of each slice's table
  • @gregcaporaso added a new visualizer called da_barplot that adds support for generating bar plots from ANCOM-BC data, inspired by Figure 6 in the ANCOM-BC paper
  • @crusher083 added a new flag in ANCOM called --filter-missing that will filter samples with missing metadata when enabled, and will produce an error that includes the IDs with missing metadata if disabled

• q2-feature-table

  • ghubrakesh authored a change that makes the language used for the summarize output more clear, changing feature count to frequency

• q2-fmt

  • @cherman2 added a Proportional Engraftment of Donor Strains(PEDS) method called sample_peds that tracks percentage of donor features that were transferred to the recipient after FMT intervention The method is further explained in Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes | Nature Microbiology.
  • @cherman2 added a new visualizer called plot_heatmap that adds support for generating a heatmap to visualize PEDS for each subject over time

• q2-stats

  • @lizgehret fixed some and associated test failures caused by API changes to the frictionless dependency

• q2-types

  • @colinbrislawn made a small update within the per_sample_sequences formats that updates the call of .iteritems to .items, since pandas will be deprecating .iteritems in the near future

• docs

  • @wasade revised the Greengenes entries to now include 2022.10, which is the latest release of Greengenes2