qiime 2.0.5: Initial End-to-End Microbiome Analysis Pipeline

We're excited to announce the 2.0.5 minor release of the QIIME 2 framework and supporting plugins. This is the first synchronized release, meaning that we intend all interfaces and plugins versioned 0.0.5 to work with QIIME 2.0.5. As always you can see the QIIME 2 ChangeLog for additional information.

The new QIIME 2 website is also now live, and contains tutorials and example data that you can use to learn QIIME 2. (This site will eventually transition to replace the current qiime.org.)

Highlights of this release include:

• Our first attempt to stabilize the .qza/.qzv archival formats, which means that we intend to support artifacts and visualizations generated by this release (2.0.5) into the future. While we expect the format to continue to evolve, we now have machinery to support future changes in backwards compatible ways.
• Significant improvements to QIIME 2's command line interface (q2cli). These include a faster response time, tab-completion of command and parameter names, per-command configuration via an .ini file, support for default values, and more.
• Default values are now supported by the framework, allowing plugin developers to indicate what parameters are not required from the user.
• Improved importing of data. It is now possible for QIIME to consume data in more than one format via the use of transformers. This means we can expand the variety of file formats that QIIME 2 will be able to consume (and existing plugins will automatically benefit from it).

This is also the first release to include an end-to-end microbiome analysis pipeline (from raw sequence data through diversity analysis statistics and interactive visualizations). The plugins that make this possible are:

• q2-demux : Demultiplex Illumina data
• q2-dada2 : Apply DADA2 to denoise sequence data, including chimera filtering and phiX filtering
• q2-feature-table : Work with feature tables (QIIME 2's equivalent of OTU Tables)
• q2-feature-classifier : Assign taxonomy to sequence reads using a variety of machine learning classifiers
• q2-taxa : Generate interactive taxonomic composition plots
• q2-alignment : Perform sequence alignment to support diversity analyses
• q2-phylogeny : Perform phylogenetic reconstruction to support diversity analyses
• q2-diversity : Compute alpha and beta diversity analysis, and generate statistics and interactive visualizations
• q2-emperor : Generate interactive principal coordinate plots
• q2-composition : Apply differential abundance testing using ANCOM

We're very grateful to all of the plugin developers who have contributed functionality to this pipeline.

Because our microbiome analysis functionality is still currently very new, QIIME 2 is not yet recommended as a replacement for QIIME 1, but we are very interested in having users test QIIME 2 and give us feedback.

In addition to user testing, we're also interested in working with developers who are interested in contributing new QIIME 2 plugins or interfaces. You should read our draft plugin developer documentation at https://2.qiime.org to get started. While QIIME 2 is in its alpha release stage, backward incompatible interface changes that impact plugins and interfaces can and will occur. We will make every effort to minimize these, and we will always document these in the QIIME 2 ChangeLog.

Finally, we're wrapping up our initial version of the QIIME 2 documentation and tutorials. We expect the new site to go live by this Tuesday, 11 October 2016. That documentation will be at http://2.qiime.org, and you'll see a placeholder at that page until the new site goes live.

As always, thanks for your interest in QIIME!