QIIME 2 2020.11 is now available!

The QIIME 2 2020.11 release is now available! Thanks to everyone involved for their hard work!

As a reminder, our next planned QIIME 2 release is scheduled for February 2021 (QIIME 2 2021.2), but please stay tuned for updates.

Check out the QIIME 2 2020.11 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 within the next week - watch this topic thread for an update!

Here’s the highlights of the release:

• General Announcements
  • A data integrity bug has been identified in the q2-cutadapt plugin, and fixed in this release of QIIME 2. For more details, please check out "Discarded results produced by q2-cutadapt's trim-paired when working with mixed-orientation reads" for more details.
  • Developer "staging" environments are now hosted on https://packages.qiime2.org! Staging environments are used during the development process, and were previously hosted on qiime2-staging | Anaconda.org. We ran into some packaging issues during this release of QIIME 2, so we bumped up priority of some of our efforts related to migrating to QIIME 2 Library - this is a solid step! Please note, we skipped the 2020.11.0 version of QIIME 2 and went straight to 2020.11.1, so when you install this release, please keep in mind that you didn't "miss" a version, we just never released the 2020.11.0 version.
  • @thermokarst and @andrewsanchez made changes to support the big pandas move from version 0.25 to version 1.0 () (pandas 1 was released earlier this year).
  • @ebolyen updated R to version 4, woohoo!
  • Docker images are now hosted on quay.io. This is because of DockerHub's recently billing-structure changes. We think quay.io will be a great new home for QIIME 2 Docker images!
• QIIME 2 Framework
  • @thermokarst fixed a developer-facing bug related to Pipeline error checking.
  • @andrewsanchez continued working on the upcoming Usage API, now there is developer-facing API documentation, type hints, as well as some general tidying up . We will announce more about the Usage API in 2021!
• User Docs
  • @ChrisKeefe, @Oddant1, and @andrewsanchez cleaned up a few typos and grammatical errors in the Parkinson's Mice tutorial!
  • @ChrisKeefe fixed some import path errors in the "Artifact API" tutorial
  • @mcmk3 added a new guide for getting set up with the Windows Subsystem for Linux, a great installation option for Windows users!
  • @thermokarst updated some "even sampling value selection" guidance in the tutorials, because some of the read-counts shuffled around a bit with the new version of DADA2.
• Dev Docs
  • @andrewsanchez added a new section of API docs for the upcoming Usage API announcement (some time in 2021).
• q2-alignment
  • @misialq added support for an --addfragments flag which optimizes for the addition of short sequence fragments (for example, primer or amplicon sequences).
• q2-cutadapt
  • @thermokarst identified and fixed a data integrity bug when demultiplexing mixed-orientation reads with the demux-paired method. More details can be found at "Discarded results produced by q2-cutadapt's trim-paired when working with mixed-orientation reads"
  • @andrewsanchez and @thermokarst made some changes to support new behavior in the 3.0 release of cutadapt in which, "demultiplexing now always generates all possible output files."
• q2-dada2
  • @ebolyen updated DADA2 from version 1.10.0 to version 1.18.0. The release notes aren't published yet, but please keep an eye on DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution for more details! Check out ReleaseNotes_1_18.utf8 for details about this release of QIIME 2 (thanks for the correction @sixvable!)
• q2-demux
  • @Oddant1 fixed a bug in the Interactive Quality Plot tabs of demux visualizations that resulted in a message stating "n out of [object Object] sequences," where [object Object] should have been the total sequence count.
  • @wasade wrestled a memory hog bug ! Now per-sequence statistics are tracked by writing to disk rather than storing in memory, which should be a nice little performance boost.
  • @wasade added a new parameter to the emp_single and emp_paired methods: ignore_description_mismatch. This parameter allows for ignoring mismatches in sequence record description fields, which can occur when sequencing runs produce mismatched description fields.
  • @thermokarst fixed a small packaging bug that could create a confusing version-identifier when running qiime info on this plugin.
• q2-diversity
  • @ChrisKeefe updated the alpha method's documentation to include a link to the scikit-bio docs, since scikit-bio is responsible for most of the heavy lifting in this method.
  • @thermokarst fixed a small packaging bug that could create a confusing version-identifier when running qiime info on this plugin.
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2-diversity-lib
  • @wasade added a new method called beta_phylogenetic_meta_passthrough, which exposes the new unifrac.meta method (see meta UniFrac). We expect to expand on this in the coming releases.
• q2-emperor
  • @yoshiki added some guards to the plot visualizer that prevents users from accidentally attempting to plot data that should be rendered with the biplot visualizer, instead!
• q2-feature-table
  • @jwdebelius created a new action to filter features based on the prevalence of the feature with a relative abundance of at least x. (For example, 0.1% in at least 10% of samples).
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2-longitudinal
  • @timanix improved the linear mixed-effects visualizations by adding padding to the figures.
• q2-phylogeny
  • @SoilRotifer added deprecation notice for IQ-TREE 2 related functionality. Don't worry, iqtree isn't going anywhere. We're simply in the process migrating iqtree related actions into a more full-featured q2-iqtree2 plugin.
• q2-quality-control
  • @thermokarst nudged our CI pipeline in the right direction by specifying a minimum version of samtools.
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2-sample-classifier
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2-taxa
  • @thermokarst fixed a small packaging bug that could create a confusing version-identifier when running qiime info on this plugin.
• q2-types
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2templates
  • @andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
• q2view
  • @fedarko fixed a typo on the homepage, !

Happy QIIMEing! :