QIIME 2 2017.11 release is now live!

The QIIME 2 2017.11 release is now live! There are lots of exciting new changes packed into this release that are described below. Through the end of 2017 we will have monthly releases. We highly recommend staying up-to-date with the latest releases to get access to new features, bug fixes, documentation, etc. We will only provide user support for the latest monthly release of QIIME 2 as these monthly releases continue through the end of 2017.

QIIME 2 will succeed QIIME 1 on January 1, 2018. QIIME 1 will no longer be officially supported at that time, as development and support effort for QIIME will be focused entirely on QIIME 2. Existing QIIME 1 users are strongly encouraged to transition from QIIME 1 to QIIME 2 now as QIIME 1 support will end in one month! :calendar:

Check out the QIIME 2 2017.11 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!

We will provide official conda builds on release day for native QIIME 2 installations. Virtual machine builds such as AWS and Docker will be released within the following week. We will post a follow-up announcement here when those builds become available.

Here’s the highlights of the release:

  • QIIME 2 Framework
    • The Choices predicate used on Str primitive types will now raise an error if it is given an empty set. Thanks @patthehat033!
  • docs
    • Added help text on how to identify valid metric values in the longitudinal tutorial.
    • Clarified how to receive support and report bugs in the “Community” section of the docs.
    • Removed link to old “Planned Plugins” spreadsheet. The best place to learn about new plugins is here, on the QIIME 2 Forum!
    • Fixed a bug in the feature-classifier tutorial: an incorrect value was suggested for the trunc-len parameter in one of the commands.
    • Trained new classifiers with sklearn 0.19.1.
    • Added tutorials for the new evaluate-composition and evaluate-seqs actions in the q2-quality-control tutorials page.
    • Added tutorials describing new features in q2-longitudinal, including spaghetti plots and measuring baseline differences/distances.
    • q2-longitudinal tutorial: provided more information on using q2-metadata to view valid metric values in artifact inputs, on interpreting linear-mixed-effects results, and fixed an inaccurate description of the z-scores provided in LME results.
  • q2-vsearch
    • A new method join-pairs has been added to join paired end sequence reads using vsearch's merge_pairs command. See the paired end reads community tutorial for more details.
    • Perform open-reference OTU picking using cluster-features-open-reference.
    • dereplicate-sequences now supports using joined sequences (SampleData[JoinedSequencesWithQuality]) and SampleData[SequencesWithQuality].
  • q2-demux
    • Support SampleData[JoinedSequencesWithQuality] as input data for the summarize visualizer. See the paired end reads community tutorial for more details.
    • Added a new transformer: EMPPairedEndDirFmt -> BarcodeSequenceFastqIterator.
  • q2-quality-filter
  • q2-deblur
  • q2-quality-control
    • Added new actions: evaluate-seqs and evaluate-composition! These actions are described in the tutorials.
  • q2-longitudinal
    • linear-mixed-effects now shows the table at the top of the visualization.
    • Exposed random slope and intercept values in linear-mixed-effects.
    • first-differences and first-distances now accept a baseline parameter which allows comparison against a value in the provided state-column instead of the previous state.
    • The volatility method can now overlay spaghetti plots in its visualization with a new spaghetti parameter.
  • q2-types
    • Added new importable type SampleData[JoinedSequencesWithQuality] for representing demultiplexed paired end sequence data that has already been joined. See the paired end reads community tutorial for more details.
    • QIIME1DemuxFormat now supports empty files.
    • Added a new transformer: SingleLanePerSampleSingleEndFastqDirFmt -> QIIME1DemuxDirFmt.
  • q2cli
    • Updated file path validation, resulting in clearer error messages of file path-related errors for users of q2cli!
  • q2studio
    • Now displays a prominent warning that it is a prototype and that some features may not work as well as its CLI counterpart (q2cli).
  • q2-gneiss
    • Fixed a bug related to recent versions of pandas.
  • q2-feature-classifier
    • Bumped the minimum version of sklearn to 0.19.1.

Happy QIIME-ing! :sun_with_face:


The QIIME 2 Virtual Machines are now available! We have QIIME 2 2017.11 available on AWS, Docker, and VirtualBox, please see the docs for more information. Thanks! :tada: