The QIIME 2 2019.10 release is now available! Thanks to everyone involved for their hard work!
As a reminder, our next planned QIIME 2 release is scheduled for late January 2020 (QIIME 2 2020.1), but please stay tuned for updates.
Check out the QIIME 2 2019.10 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:
QIIME 2 Framework
@Oddant1 added a
viewmethod to the
BinaryFileFormatclasses, which allows for easier type conversion (especially for developers!).
- @Nicholas_Bokulich updated the citation info for the canonical QIIME 2 citation (Bolyen et al., 2019 Nature Biotechnol)
- @David-Rod upgraded our core distribution to use the latest (and greatest) version of Pandas !
- @Oddant1 implemented a highly sought after feature - Metadata constructed via the Artifact API now gets all of its whitespace stripped off ! This is really useful for the dozens of transformers that allow for various semantic types to be “viewed” as Metadata!
@ebolyen fixed a bug that prevented
MetadataColumnvalues from being decoded properly - this was mostly an issue for q2studio.
@thermokarst made some changes to a framework utility that uses the
networkxpackage — QIIME 2 is now compatible with the latest release of this tool!
- @Oddant1 added a
@Nicholas_Bokulich updated the tutorials to reflect changes to the
feature-table heatmapAPI (primarily the parameter rename from
- @SoilRotifer added the tutorial Phylogenetic inference with q2-phylogeny. This is the latest version of his Community Tutorial of the same name
- @BenKaehler added a nifty new section to the Parkinson’s Mice Tutorial that demonstrates how to create a bespoke classifier.
- @ChrisKeefe found a pesky typo in the Parkinson’s Mice Tutorial dataset , but fortunately those days are behind us!
- @thermokarst created a new “SEPP Refs” section of the Data Resources page on the QIIME 2 Docs - these handy little databases are for use with q2-fragment-insertion!
- @gregcaporaso re-wrote the User Glossary of QIIME 2 terms - if you have ever puzzled over our definitions of words like “Artifact” or “Pipeline” - this is the page for you!
- @Nicholas_Bokulich updated the tutorials to reflect changes to the
- @ebolyen, chief drop-shadow design guru for the QIIME 2 team did what he does best: beefed up the drop shadow on the Library!
- @David-Rod fixed a bug that caused help text generation to slow down significantly! For the average user this wasn’t much of a problem, but, if you’re in the business of building QIIME 2 docs, this slowdown was significant.
- @Oddant1 fixed a bug that prevented exporting to a local path. We think Rumpelstiltskin was involved - but that’s neither here nor there - @Oddant1 got us sorted out!
- @ebolyen fixed a bug that caused things to explode when saving files into a non-existent directory!
- @Oddant1 improved the error message presented when an invalid primitive value is identified — previously the error message was pretty opaque, now it actually tells you what is wrong!
@Oddant1 added the
heatmapvisualizer to the party known as the
@Nicholas_Bokulich fixed a bug in
confusion-matrixthat caused ROC plots to fail on unstratified, imbalanced data.
cividisto the list of available colormaps.
@Oddant1 added the ability to adjust color scale of the
- @David-Rod made some updates to the transformers defined in this plugin to allow it to work with the latest versions of Pandas !
@Nicholas_Bokulich added a new
drop_all_uniqueparameter to the
metatableaction - this prevents metadata with all unique columns from ruining the party
@ChrisKeefe fixed a bug in the
heatmapvisualizations produced in this plugin that caused some cells to be trimmed, which looked pretty weird!
- @Oddant1 added the
cividisto the list of available colormaps. Wow, @Nicholas_Bokulich was really excited about this colormap!
@Nicholas_Bokulich made the
plot-feature-volatilityvisualization a lot more performant by building-in a simple “filter” system - by default only the top 100 most important features will be displayed. There are a few other mechanisms for filtering importances - check out the docs here!
- @Nicholas_Bokulich added
@David-Rod removed white space and comment support from
TSVTaxonomyFormat. These elements generally caused more problems than they solved, so we decided to part ways with those aspects of the formats.
@Oddant1 made it so
DNAFASTAFormatdisallows duplicate records, disallows whitespace at the start of an ID, and a few other housekeeping elements.
- @David-Rod made some updates to the tests defined in this plugin to allow it to work with the latest versions of Pandas !
@David-Rod beefed up the validation for
TSVTaxonomyFormat- users will be presented with much clearer error messages whenever there is a problem importing or creating one of these files!
- @David-Rod removed white space and comment support from
- This release is using the latest release version of emperor (
- Miscellaneous bug fixes: and performance improvements :
- Improve error messages for missing or mismatching feature metatdata.
- For large plots fix a problem where hidden objects would still be clickable.
- Fixes a bug where axes orientation would be incorrectly loaded from a settings file.
- Daniel Hakim: Improved performance for animations with a large number of timepoints.
- New features :
- Add a search bar to every tab to narrow down the values you are interested in for any metadata column.
- Xuhan Yang: Adds a list of colors to the color selector based on the currently selected color palette.
Daniel Hakim: Add the ability to visualize multiple dimensions using parallel plots. Go to the Axes tab and click on
Scatterto change the plot type.
- The following animated GIF showcases all three new features:
- This release is using the latest release version of emperor (
@tomasz implemented a new
intersect_idsfeature in the
alpha-correlationvisualizer. This parameter allows for filtering out IDs in sample metadata or the
SampleData[AlphaDiversity]that aren’t found in both inputs (which would previously terminate as an error).
@yoshiki got the
core-metrics-phylogeneticspipelines outfitted with the ability to
@ebolyen fixed a bug in the
beta-group-significancevisualization that caused some of the boxplots and PDFs to not show up. This was primarily caused by having any kind of non-alphanumeric characters in the metadata used to compute the visualization:
- @tomasz implemented a new
@colinbrislawn hooked us up with a sweet new feature in
join-pairs— the ability to specify how many execution threads with which to get the job done! Neat!
- @colinbrislawn hooked us up with a sweet new feature in
@David-Rod took a magnifying glass to the
barplotvisualizer in this plugin - lo and behold, a simple, yet important typo was revealed - an error used the word “feature” when it should’ve used the word “sample”. Funny how such a small change in language can yield such different results!
- @David-Rod took a magnifying glass to the
@thermokarst & @Stefan brought SILVA 128 to the
seppmethod, and there was much rejoicing! This method no longer contains a “default” reference (it used to be GreenGenes) - now users can grab a handy SEPP database reference from the Docs (pick your favorite - SILVA or GG!). In the future we hope to expose new methods to support importing and prepping any database, stay tuned ! For a glimpse of this new action, well, uh, in action, check out the Parkinson’s Mouse Tutorial!
- @thermokarst & @Stefan brought SILVA 128 to the
@Oddant1 updated the
DADA2StatsFormatto include a few new computed columns, that way you don’t have to do the mental math to figure out the percentage of reads merged. Phew!
- @Oddant1 updated the