QIIME 2 2022.2 is now available!

The QIIME 2 2022.2 release is now available! Thanks to everyone involved for their hard work!

As a reminder, our next planned QIIME 2 release is scheduled for April, 2022 (QIIME 2 2022.4), but please stay tuned for updates.

Check out the QIIME 2 2022.2 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!

Virtual machine builds will be available sometime this week (except for q2galaxy, its docker container is already published) - watch this topic thread for an update!

New Documentation:

This release is timed with the release of several QIIME 2 documentation projects that provide new ways to learn QIIME 2 now, and a glimpse into where we're headed with QIIME 2 documentation in the future.

• We're excited to share a new multiple interface QIIME 2 tutorial, the Cancer Microbiome Intervention tutorial. This tutorial derives from data from over 12,000 human-cancer-associated microbiome samples published in 2021 in Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Users can choose whether to follow along using the QIIME 2 Galaxy Interface (which you can learn how to install here), the QIIME 2 command line interface, or the Python 3 API. This content is provided as a JupyterBook, a documentation tool that you can expect to see a lot more of around the QIIME 2 ecosystem.
• A new, free QIIME 2 YouTube course that parallels the Cancer Microbiome Intervention tutorial. Over the next several months, we'll release new videos each week. This is our first video tutorial series that focused on the Galaxy interface, so if you want to learn to use QIIME 2 through Galaxy, this is a great place to start! @gregcaporaso provides a 3.5 minute introduction to the course here.
• @gregcaporaso is sharing a preview of his QIIME 2 JupyterBook, q2book. This is a work-in-progress, and not yet complete, but you can find useful background on QIIME 2 archives (i.e., .qza and .qzv files), semantic types, importing, and more topics that will help you deepen your understanding of how QIIME 2 works and why.
• Our Jupyter Book based tutorials (mentioned above), can be found on a new page in our user documentation, titled Jupyter Book Tutorials.

Additional features:

• QIIME 2 Framework
  • @ChrisKeefe made a handful of improvements/tweaks to Usage
  • @ebolyen fixed an inconsistency in the view_type parameter of Usage.import_from_format, both string and classes are accepted as arguments now
  • Artifact API has now been renamed to the Python3 API
• q2cli
  • @ebolyen fixed a bug in the Usage driver which resulted in a namespace collision
  • @ebolyen fixed an issue where the incorrect usage variable was returned for Usage.view_as_metadata
• q2galaxy
  • When installing q2galaxy via the pre-built docker image, the conda environment is now already included. This results in a larger base image, but makes it far less likely that installation will fail. As a result, the first job will no longer take in excess of 40 minutes to complete
  • @ebolyen added a new Usage driver to automatically generate RST instructions for use within Galaxy tools and documentation
  • @ebolyen fixed an issue with string sanitization in the generated tools. (Unusual characters like ; would be silently converted, breaking functionality.)
  • @ebolyen added a new template function to provide an automatically nested and alphabetized tool_conf.xml file. See q2galaxy template tool-conf --help
• q2-sample-classifier
  • @misialq added cross-validation to KNN sample classification based on distance matrices
• q2-dada2
  • @sixvable added support for PacBio CCS data and @Keegan-Evans and @lizgehret added some final tweaks and tests + data. For more details be sure to checkout @benjjneb's DADA2 paper (and datasets!) that this is a wrapper for
• q2-longitudinal
  • @ebolyen added support for automatically quoting formula terms in linear-mixed-effects. Now column names like my-category will be quoted as Q('my-category') instead of raising an error.
• q2-mystery-stew
  • @ebolyen added more sophisticated metadata interactions. Now tests include Usage.view_as_metadata and Usage.merge_metadata

Happy QIIMEing!