The QIIME 2 2020.6 release is now available! Thanks to everyone involved for their hard work!
As a reminder, our next planned QIIME 2 release is scheduled for August 2020 (QIIME 2 2020.8), but please stay tuned for updates.
Check out the QIIME 2 2020.6 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!
BREAKING CHANGES
- q2-diversity
core_metrics_phylogenetic: Then_jobsparameter has been renamedn_jobs_or_threadsto accommodate a speedy new implementation of unifrac now being usedcore_metrics&core_metrics_phylogenetic: The phraseobserved_featuresis replacingobserved_otus, as "observed features" better describes the different ways in which users work with non-taxonomic features in QIIME 2 (an OTU is a feature, but a feature isn't necessarily an OTU)core_metrics&core_metrics_phylogenetic:n_jobsandn_jobs_or_threadsno longer accept zero or negative integers as arguments. Users should passautoto those parameters to use all available physical cores
Highlights of the release:
- QIIME 2 Framework
- @thermokarst, @andrewsanchez, and @David-Rod worked up further developing the
Usage API, which will allow plugin developers to showcase usage examples of their plugin actions, in an interface agnostic way!
This included:- Enabling source tracking of initialized data
- Adding a method to initialize data collections
- @thermokarst improved some of the developer documentation in the test harness.
- @Oddant1 increased level of validation of filenames to prevent creation of artifacts with incorrectly named data files.
- @thermokarst, @andrewsanchez, and @David-Rod worked up further developing the
- docs
- @ChrisKeefe showed us how to
peekat an Artifact in the Moving Pictures Tutorial
- @ChrisKeefe added a section to the Importing Tutorial for multiplexed fastq files with barcodes in sequences.
- @ChrisKeefe clarified the behaviors of
qiime tools viewand q2view
- @thermokarst added Native installation instructions for Windows users leveraging the Windows Subsystem for Linux
- @thermokarst added some rough guidelines for selecting an installation method that best fits your computational needs
- @thermokarst added examples of
q2-demux's subsampling and sample filtering tools to the Atacama tutorial
- @Oddant1 Changed the wording of the suggestion to use the vega editor for the q2-longitudinal volatility plot to reflect the current implementation
- Several small typos were fixed, including one by
@hmaru (GH)!
- @thermokarst overhauled the User Docs hosting infrastructure.
- @ChrisKeefe showed us how to
- data-resources
- @Nicholas_Bokulich also added SILVA 138 release sequence and taxonomy files formatted for use with QIIME 2. Data were prepared and formatted using RESCRIPt (co-developed with @SoilRotifer)! See that tutorial for more details on how these files were generated, and a pipeline to reproduce this process!
- @Nicholas_Bokulich added new pre-trained classifiers for Greengenes 13_8 release and SILVA 138 release (the latest versions of both), trained using scikit-learn 0.23.1. These classifiers were built and tested in a new way, using RESCRIPt!
- @Nicholas_Bokulich also added SILVA 138 release sequence and taxonomy files formatted for use with QIIME 2. Data were prepared and formatted using RESCRIPt (co-developed with @SoilRotifer)! See that tutorial for more details on how these files were generated, and a pipeline to reproduce this process!
- q2cli
- @thermokarst fixed up an error message: a tiny typo can cause a surprising amount of confusion!
- @andrewsanchez merged in the first iteration of the Usage API CLI driver
. This should be considered as sort of "pre-release," for developers until the Usage API and usage examples are a bit more mature. Stay tuned for much more action in this realm in future releases!
- @thermokarst fixed up an error message: a tiny typo can cause a surprising amount of confusion!
- QIIME 2 Studio
- @andrewsanchez fixed a bug that cropped up when trying to import data!
- @andrewsanchez fixed a bug that cropped up when trying to import data!
- q2-feature-classifier
@cherman2(GH) helped remind us why we don't have multithreading options for the blast classifier - thanks for the research and code comments!
@adamovanja(GH) added atrim-rightoption to theextract-readsaction, allowing simulated reads to be trimmed at the 3' ends. This is useful for, e.g., emulating trimming options of reads coming from q2-dada2, to generate optimally trimmed reference sequences for classifier training as described here. Thank you adamovanja for fixing this issue, and @Sean_McKenzie for bringing it to our attention!
- @Nicholas_Bokulich improved the docs for
extract-reads
! - @Nicholas_Bokulich trained new feature-classifiers using scikit-learn 0.23.1
- q2-phylogeny
- @ebolyen added a new method,
robinson-foulds, for comparing two phylogenetic trees!
- @ebolyen added a new method,
- q2-composition
- @thermokarst fixed a bug in
ancom! The visualization had a propensity for (accidentally) attempting to divide by zero - never a good plan! - @Oddant1 Removed the link to the vega editor on the ancom plot pending a rework of the plot for vega 5
- @thermokarst fixed a bug in
- q2-cutadapt
- @Oddant1 and @thermokarst added support for demultiplexing mixed-orientation single-indexed reads.
- @Oddant1 and @thermokarst added support for demultiplexing mixed-orientation single-indexed reads.
- q2-feature-table
- @David-Rod added some usage examples to the
mergemethod!
- @jwdebelius added a new method for re-naming features or samples in a table
- @thermokarst fixed a bug that caused
summarizevisualizations to sometimes display distorted column widths
- @Oddant1 Removed the link to the vega editor on the summarize plot pending a rework of the plot for vega 5
- @David-Rod added some usage examples to the
- q2-alignment
- @gregcaporaso added a new action,
mafft-add, which allows for the addition of unaligned sequences to an existing alignment
- @gregcaporaso added a new action,
- q2-quality-filter
- @thermokarst merged
q-scoreandq-score-joinedinto the same method (q-score), and deprecated theq-score-joinedmethod. This method will be removed in the fall 2020 release of QIIME 2.
- @thermokarst merged
- q2-quality-control
- @Nicholas_Bokulich (aka Doc Bok) added a new
filter_readsmethod that supports filteringSampleData[SequencesWithQuality]andSampleData[PairedEndSequencesWithQuality]artifacts (a.k.a. FASTQ sequence data) by alignment to a reference database. How might you use this? To filter human reads and other non-target (or junk) sequences prior to denoising or dereplication. - @gwarmstrong transitioned
alpha_phylogeneticandalpha_rarefactionto use Stacked Faith, a speed- and memory-optimized implementation previous available inalpha_phylogenetic_alt.alpha_phylogenetic_altwill be removed in the next release.
- @Nicholas_Bokulich (aka Doc Bok) added a new
- q2-diversity
@patrickimran (GH)added a newjensenshannonbeta diversity metric!
- @ChrisKeefe wired up q2-diversity-lib to perform alpha- and beta-diversity calculations for
core-metricsandcore-metrics-phylogenetic. See Breaking Changes above for related API changes. - @Oddant1 fixed a bug allowing 0 variance numerical columns to slip past the filter in
bioenvcausing errors.
- q2-diversity-lib
- @ChrisKeefe - this
plugin calculates alpha- and beta-diversity measures, expands the number of available semantic types where appropriate, and provides measure-specific citation information.
- @ChrisKeefe - this
- q2-types
- @thermokarst added new transformers for working with per-sample-sequences in fun and interesting ways (dev alert!)
- @gregcaporaso added more aligned sequence transformers.
- @thermokarst added new transformers for working with per-sample-sequences in fun and interesting ways (dev alert!)
- q2-vsearch
- @thermokarst fixed up a performance bug in the
cluster-features-closed-referencemethod, resulting in potentially significant speedups for some use-cases. - @angrybee (gh) added an awesome new visualizer
fastq_statsfor distilling single-end or paired-end sequences into FASTQ file statistics using vsearch!
- @Oddant1 added the ability for all vsearch methods to accept sequences shorter than 32nt
- @Oddant1 set
--fasta_width 0on invoked vsearch commands to prevent fasta records from being split across multiple lines
- @thermokarst fixed up a performance bug in the
- q2-longitudinal
- @Oddant1 removed the link to the vega editor from the volatility plot pending a rework of the plot for vega 5
- q2-demux
- @Oddant1 and @thermokarst reworked summarize visualization to better inform the user of missing reads
- q2-dada2
- @benjjneb added pseudo-pooling to all DADA2 workflows, allowing users to increase sensitivity to rare variants in samples, particularly singletons, as long as they were observed in other samples independently.
- @ebolyen squashed a bug where feature-tables containing only one feature were being mis-diagnosed as empty.
- q2-sample-classifier
- @Nicholas_Bokulich gave the test suite some much needed TLC with a generous refactor.
- @Nicholas_Bokulich gave the test suite some much needed TLC with a generous refactor.
- q2-emperor
- @yoshiki and @antgonza updated to the latest release of Emperor 1.0.1
. - @yoshiki fixed an issue where biplot arrows would incorrectly show while visualizing a parallel plot.
- @fedarko fixed an issue where continuous and divergent colormaps would be partially used in categorical data.
- @fedarko fixed a bug with sorting numeric and non-numeric values.
- @yoshiki fixed an issue where axes settings wouldn't load correctly from the Python API.
- @fedarko and @yoshiki updated various dependencies.
- Added the ability to select a group of samples and save the sample names to the users' clipboard. To do this, users need to hold shift and select the samples they are interested in:
- @yoshiki and @antgonza updated to the latest release of Emperor 1.0.1
Happy QIIMEing! 
