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
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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 anaconda.org/qiime2-staging. 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!
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QIIME 2 Framework
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@thermokarst fixed a developer-facing bug related to
Pipelineerror 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!
-
@thermokarst fixed a developer-facing bug related to
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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.
-
@ChrisKeefe, @Oddant1, and @andrewsanchez cleaned up a few typos and grammatical errors in the Parkinson’s Mice tutorial!
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Dev Docs
-
@andrewsanchez added a new section of API docs for the upcoming Usage API announcement (some time in 2021).
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@andrewsanchez added a new section of API docs for the upcoming Usage API announcement (some time in 2021).
-
q2-alignment
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@misialq added support for an
--addfragmentsflag which optimizes for the addition of short sequence fragments (for example, primer or amplicon sequences).
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@misialq added support for an
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q2-cutadapt
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@thermokarst identified and fixed a data integrity bug when demultiplexing mixed-orientation reads with the
demux-pairedmethod. 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.”
-
@thermokarst identified and fixed a data integrity bug when demultiplexing mixed-orientation reads with the
-
q2-dada2
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@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 https://benjjneb.github.io/dada2/ for more details!Check out https://benjjneb.github.io/dada2/ReleaseNotes_1_18.html for details about this release of QIIME 2 (thanks for the correction @sixvable!)
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@ebolyen updated DADA2 from version 1.10.0 to version 1.18.0.
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q2-demux
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@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_singleandemp_pairedmethods: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 infoon this plugin.
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@Oddant1 fixed a bug in the Interactive Quality Plot tabs of demux visualizations that resulted in a message stating “n out of
-
q2-diversity
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@ChrisKeefe updated the
alphamethod’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 infoon this plugin.
-
@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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@ChrisKeefe updated the
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q2-diversity-lib
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@wasade added a new method called
beta_phylogenetic_meta_passthrough, which exposes the newunifrac.metamethod (see meta UniFrac).
We expect to expand on this in the coming releases.
-
@wasade added a new method called
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q2-emperor
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@yoshiki added some guards to the
plotvisualizer that prevents users from accidentally attempting to plot data that should be rendered with thebiplotvisualizer, instead!
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@yoshiki added some guards to the
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q2-feature-table
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@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).
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
-
@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).
-
q2-longitudinal
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@timanix improved the linear mixed-effects visualizations by adding padding to the figures.
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@timanix improved the linear mixed-effects visualizations by adding padding to the figures.
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q2-phylogeny
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@SoilRotifer added deprecation notice for IQ-TREE 2 related functionality. Don’t worry,
iqtreeisn’t going anywhere. We’re simply in the process migratingiqtreerelated actions into a more full-featuredq2-iqtree2plugin.
-
@SoilRotifer added deprecation notice for IQ-TREE 2 related functionality. Don’t worry,
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q2-quality-control
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@thermokarst nudged our CI pipeline in the right direction by specifying a minimum version of samtools.
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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@thermokarst nudged our CI pipeline in the right direction by specifying a minimum version of samtools.
-
q2-sample-classifier
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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q2-taxa
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@thermokarst fixed a small packaging bug that could create a confusing version-identifier when running
qiime infoon this plugin.
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@thermokarst fixed a small packaging bug that could create a confusing version-identifier when running
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q2-types
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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q2templates
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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@andrewsanchez & @thermokarst updated various aspects of this plugin to support pandas 1.0!
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q2view
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@fedarko fixed a typo on the homepage,
!
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@fedarko fixed a typo on the homepage,
Happy QIIMEing! 
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