The QIIME 2 2017.9 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 supported at that time, as development and support effort for QIIME will be focused entirely on QIIME 2. We recommend that existing QIIME users begin transitioning from QIIME 1 to QIIME 2 now.
Check out the QIIME 2 2017.9 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. 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
- Artifacts and Visualizations now record their
output-namein provenance. This can help consumers of provenance disambiguate multiple artifacts produced by the same Action (e.g.qiime diversity core-metrics).
FileFormats andDirectoryFormats can now implement avalidatemethod which may raise aValidationErrorto explain what part of a given file/directory makes it invalid.- Added additional validation and cleanup to TSV-format metadata files - rows made entirely of whitespace will be ignored (like they are with a comment line).
- Artifacts and Visualizations now record their
- docs
- Updated the Sample Classifier tutorial to include an example of
maturity-index, as well as replaced the Atacama dataset with ECAM. - Updated the Longitudinal tutorial to include an example of
volatility, as well as using the ECAM dataset now.
- Updated the Sample Classifier tutorial to include an example of
- q2-vsearch
- This new plugin wraps several
vsearchmethods, allowing for dereplication as well as de novo and closed-reference OTU picking!
- A Community Tutorial for de novo and closed-reference OTU picking with
q2-vsearchis now available. This will be transitioned to the QIIME 2 docs in a future release.
- This new plugin wraps several
- q2-longitudinal
- Warnings are now displayed in a collapsible section in the visualization instead of
stdout. - Fixed a bug in
linear-mixed-effectsthat caused it to fail when only one variable was provided as input. - LME now fails gracefully when singular matrix error is raised.
- Added
volatilityvisualizer, which lets you plot a control chart of a single dependent variable across multiple groups contained in a sample metadata column. - Fixed a bug that caused a misleading HTML title to be displayed in visualizations produced by this plugin.
- Added
nmitmethod, which performs nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. Thanks Yilong Zhang!
- Warnings are now displayed in a collapsible section in the visualization instead of
- q2-sample-classifier
- Added the ability to collapse the (sometimes lengthy) "Feature Importance" table of the
classify-samplesvisualizer. - Fixed a bug that caused a misleading HTML title to be displayed in visualizations produced by this plugin.
- Added the ability to collapse the (sometimes lengthy) "Feature Importance" table of the
- q2-feature-classifier
- Added optional
class_weightinput to sklearn classifier fitting. - Fixed a bug for classifiers that don't support confidence calculations.
- Added parameter descriptions to
classify-sklearn. - Renamed the
chunk-sizeparameter ofclassify-sklearntoreads-per-batch.
- Added optional
- q2-composition
- The
statistical-testparameter has been removed fromancom. This parameter did not generally work (resulted in an immediate error). It may be added back in the future. ancomnow provides a message when no significant features are found instead of an empty table.ancomwill now display a message if a volcano plot cannot be drawn.
- The
- q2-types
- A new semantic type
SampleData[Sequences]has been added. This has a default format ofQIIME1DemuxFormat(and is the analogue toseqs.fnafromsplit_libraries.py). DNAFASTAFormatnow supports empty files (zero FASTA records).- Fixed a bug in the
pd.SeriestoDNAFASTAFormattransformer
. CasavaOneEightSingleLanePerSampleDirFmtand related formats have been made significantly more robust and will now report issues such as missing forward/reverse reads, duplicate sample IDs, and unusual directory structures at import time.
- A new semantic type
- q2-feature-table
- Added
qiime feature-table heatmapvisualizer for visualizing a feature table as a heatmap, optionally in the context of sample metadata and sample/feature axes clustering. - Added y-axis labels to the frequency plots in the
summarizevisualizer! - Added
qiime feature-table filter-seqsto support filteringFeatureData[Sequences]. - Added a new
mergemethod:sum. This allows for both overlapping Sample IDs and Feature IDs when merging two tables.
- Added
- q2-phylogeny
fasttreemethod now supports ann-threadsparameter for runningFastTreein multi-threaded mode (usesFastTreeMPto accomplish this).
- q2-diversity
core-metricsnow computes only non-phylogenetic metrics (so a phylogenetic tree is not required as input). Addedcore-metrics-phylogeneticwhich computes both phylogenetic and non-phylogenetic metrics and requires a tree as input.core-metricsandcore-metrics-phylogeneticnow output the rarefied table in addition to the other outputs.- Fixed a bug in
alpha-rarefactionthat caused visualizations produced with optional metadata to display the sum of the various metrics, instead of the median. - A new method
beta-phylogenetic-althas been added. Notably, this method is faster and uses much less memory while producing identical results tobeta-phylogenetic, making it ideal for large datasets. This method also includes support for Generalized UniFrac and Variance Adjusted UniFrac. At a later date, this may be merged withbeta-phylogenetic. alpha-rarefactionnow ignores metadata columns that contain entirely "null" values and provides a warning indicating which columns those were.
- q2cli
- Fixed a bug where
--helptext labeled output visualizations as both Artifacts and Visualizations. qiime tools importerror messages are now formatted in a more user-friendly way.- Input options are now ordered to match the signature of the registered action, this means that required options will appear first in the help text followed by optional options and then outputs.
- Provide prettier errors when attempting to use invalid metadata (either TSV or QZA format).
- Fixed a bug where
- q2-emperor
-
Upgraded to the latest version of Emperor, which includes the following changes:
Opacity Tab (new):
- Add the ability to modify the opacity of the elements on screen, see the
Opacitytab. This tab works very much the same way as theScaletab, the opacity of the objects can be set on a per-category basis, globally (all at once), or based on a numeric metadata category.
Axes Tab:
- Add the ability to hide axes lines and axes labels. Go to the
Axestab, click on the color for the tab and then select theXon the top right of the color selector. - The bars in the scree plot (under the
Axestab) will now display the percentage explained by each dimension. - Add the ability to create 2D plots. To do this, go to the
Axestab, click on the dropdown menu for "Axes 3" and then selectHide (make 2D plot).
The animated gif below shows the tooltips for the scree plot, then how to hide the axes lines and finally how to convert the 3D plot into a 2D plot:
Bug Fixes:
- Fix a bug where the background and axes color controllers would stop working after loading a settings file.
- Fix a bug where after setting the background color to a value that is not black, the background would no longer change back to black.
- Fix a bug where attribute editors would sometimes need to be double or tripled clicked for the editors to show.
Miscellaneous:
- The tabs have been reordered, from [
Color,Visibility,Shape,Axes,Scale] to [Color,Visibility,Opacity,Scale,Shape,Axes] - Most elements on the UI now display a tooltip whenever the mouse hovers over them.
- Add a counter of visible samples on the top left of the plot.
- Add the ability to modify the opacity of the elements on screen, see the
-
Happy QIIME-ing! 
