The QIIME 2 2018.8 release is now live! There are lots of exciting new changes packed into this release that are described below.
Our next planned QIIME 2 release is tentatively scheduled for October(ish) 2018 (QIIME 2 2018.10), but please stay tuned.
Check out the QIIME 2 2018.8 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 2 if you run into any issues!
Virtual machine builds will be available sometime next week.
Here’s the highlights of the release:
- QIIME 2 Framework
- @ChrisKeefe - When calling docstrings through the Artifact API, arguments now appear in the same order used in the function signature itself, making documentation more intuitive and creating parity with the CLI.
- docs
- @turanoo - Updated the tutorial docs to reflect the new flags added to
qiime tools (import|export|extract)
. - @John_Chase - Added metadata example to the Artifact API interface page.
- @turanoo - Fixed a typo in the OTU Clustering tutorial.
- @ChrisKeefe - Plugin and Action pages in the docs now include import statements to make access more transparent for users of the Artifact API, and copy-buttons for convenience.
- @turanoo - Modified the Moving Pictures tutorial to reflect the addition of a new pipeline in
q2-phylogeny
. - @Nicholas_Bokulich - Updated the
q2-sample-classifier
tutorial to describe various new methods, changes in outputs, and add FLOWCHARTS! - @Nicholas_Bokulich - Updated the
q2-feature-classifier
tutorial to describe requirements that reference sequences and taxonomy should be paired. - @Nicholas_Bokulich - Updated the diversity analysis flowchart in the overview tutorial to show where feature table subsampling occurs in the
core-metrics*
pipelines. - @Nicholas_Bokulich - Updated the
q2-longitudinal
tutorial to describe the new actions added to that plugin in this release. - @lisa55asil - Updated the
gneiss
tutorial - @colinbrislawn - Added "updating by installing again" instructions to the install docs.
- @turanoo - Updated the tutorial docs to reflect the new flags added to
- q2view
- @turanoo - Added more examples to the gallery
- q2-diversity
- @ChrisKeefe - In 2017, the beta-correlation pipeline was split into two separate functions distance-matrix and mantel. A new beta-correlation pipeline recreates the original functionality.
- @HannesHolste - Added an approximation method to PCoA to dramatically improve the computational performance for large distance matrices (tens of thousands of samples). A new parameter in
qiime diversity pcoa
lets users specify the number of dimensions you want to compute, by default all dimensions are computed (as in previous versions of QIIME). - @Yoshiki - Added
qiime diversity pcoa-biplot
to compute PCoA biplots that project a feature table into an ordination space. - @thermokarst - Fixed a problem in the alpha-rarefaction visualization that prevented scrolling on the legend.
- @mortonjt - Added
aitchison
distance as a new metric tobeta
. This change adds an optionalpseudocount
parameter to the method. - @yoshiki - Added
permdisp
as a method forbeta-group-significance
. - @jakereps - Improved error message when metadata is empty as a result of filtering.
- q2cli
- Tab completion is now automatically available after activating your conda environment in bash and ZSH.
- Breaking changes in
q2cli
As part of our efforts to keep the builtin commands ofq2cli
consistent we have updated the subcommands available under thetools
category. The commands impacted are:qiime tools import
qiime tools export
qiime tools extract
Please update your workflows accordingly (e.g. scripts, helper commands, etc.).
Details of the changes are presented below:
qiime tools import
old:
qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path pe-64-manifest \ --output-path paired-end-demux.qza \ --source-format PairedEndFastqManifestPhred64
new:
Please note that--source-format
has been renamed to--input-format
.qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path pe-64-manifest \ --output-path paired-end-demux.qza \ --input-format PairedEndFastqManifestPhred6
qiime tools export
old:
qiime tools export \ unrooted-tree.qza \ --output-dir exported-tree
new:
Please note the positionalINPUT
argument has been replaced with an
--input-path
option, and the--output-dir
option has been renamed to
--output-path
.qiime tools export \ --input-path unrooted-tree.qza \ --output-path exported-tree
qiime tools extract
old:
qiime tools extract \ feature-table.qza \ --output-dir extracted-feature-table
new:
Please note the positionalINPUT
argument has been replaced with an
--input-path
option, and the--output-dir
option has been renamed to
--output-path
.
Thanks @turanoo!qiime tools extract \ --input-path feature-table.qza --output-path extracted-feature-table
- @turanoo -
qiime tools export
now supports exporting a file or a directory into another format. - @turanoo - Built-ins now support printing a success message after completion of a command.
- q2-quality-control
- @Nicholas_Bokulich - fixed a bug where the TAR and TDR values were transposed in
evaluate-composition
. See this post for more details.
- @Nicholas_Bokulich - fixed a bug where the TAR and TDR values were transposed in
- q2-sample-classifier
- @Nicholas_Bokulich - Added two new visualizers —
scatterplot
andconfusion-matrix
— to plot accuracy results from regressors and classifiers, respectively. - @Nicholas_Bokulich - Random splitting into training/test data is now performed on the metadata, not on the feature table. Effect on users: faster, lower memory, more efficient splitting!
- @Nicholas_Bokulich -
classify-samples
andregress-samples
are now Pipelines! Effect on users: multiple different outputs are now produced, including trained classifiers for re-use! - @Nicholas_Bokulich - API Breaking Changes
predict
has been split into two methods:predict-classification
andpredict-regression
; and theSampleEstimator
semantic type now must be eitherSampleEstimator[Classifier]
orSampleEstimator[Regressor]
formats. This makes up/downstream handling more transparent for users. - @Nicholas_Bokulich - New visualizers
Summarize
for extracting parameter settings and RFE results from trained SampleEstimators. - API Breaking Changes @Nicholas_Bokulich -
maturity-index
is no longer an action in q2-sample-classifier, it is now a pipeline in the q2-longitudinal plugin! (see below for more details). - A new pipeline,
classify-samples-from-dist
, has been added. This uses a kNN classifier to classify samples on a precomputed distance matrix, rather than from a feature table. Thanks Justin Kuczynski and Alena Kuczynski for creating this action!
- @Nicholas_Bokulich - Added two new visualizers —
- q2-types
- @HannesHolste and @Yoshiki - bumped
scikit-bio
to the latest version,0.5.4.
- @Pauline_Trinh - Added the ability for
AlphaDiversityFormat
to contain additional columns as metadata. - @gregcaporaso - Updated the alpha diversity format transformer to include metadata.
- @cduvallet - Added
PercentileNormalized
as a varient forFeatureTable
.
- @HannesHolste and @Yoshiki - bumped
- q2-phylogeny
- @SoilRotifer - Added new tree-building methods based on IQ-TREE!
- @SoilRotifer - Added access to SSE3 / AVX2 versions of RAxML via
--p-raxml-version
. These CPU-optimized versions of RAxML will reduce run time. - @turanoo - Added a new pipeline to build phylogenetic trees using mafft and fasttree.
- q2-alignment
- @turanoo - Updated
q2-alignment mafft
unit tests to remove issue caused by a newer MAFFT version. - @turanoo - Added the
parttree
parameter tomafft
allowing alignments of greater than 1 million sequences in the QIIME 2 plugin. - @turanoo - Fixed a regression in the
n-threads
parameter that prevented MAFFT from using all cores.
- @turanoo - Updated
- q2-gneiss
- API Breaking Changes
ilr-transform
has been replaced byilr-hierarchical
andilr-phylogenetic
. Thanks @qiyunzhu!- This plugin no longer makes use of the
FeatureTable[Composition]
type, instead pseudocounts have been added as parameters to the following methods:ilr-hierarchical
ilr-phylogenetic
balance-taxonomy
dendrogram-heatmap
correlation-clusterin
- Additionally the pseudocount behavior now defaults to replacement of
0
values with0.5
. This can be adjusted with thepseudocount
parameter. This value is not added to non-zero observations (like incomposition add-pseudocount
).
- API Breaking Changes
- q2-longitudinal
- Added a new pipeline,
feature-volatility
for identifying features that are predictive of sampling time (or other continuous metadata) — see the tutorial for details! Thank you @thermokarst for building theplot-feature-volatility
visualizer, the crowning gem of this pipeline. - @Nicholas_Bokulich -
individual_id_column
is now an optional parameter for the visualizervolatility
! This means thatvolatility
can be used for visualizing changes in metrics across any type of continuous data, not only longitudinal experiments where the same subjects were sampled repeatedly! - @Nicholas_Bokulich - updated
state_column
parameter descriptions for several methods to specify how that metadata column is handled by paired-sample vs. longitudinal methods. - API Breaking Changes @Nicholas_Bokulich -
maturity-index
, formerly in q2-sample-classifier, is now a pipeline in the q2-longitudinal plugin! This is because it is almost exclusively a longitudinal method (and so it was designed to be). Additionally, it is now a pipeline and the outputs and tests performed internally have been modified (and improved) extensively.
- Added a new pipeline,
- Virtual Machines
- @johnbradley - More versatile configuration of Docker image!
- q2-vsearch
- @colinbrislawn - Added
--derep_prefix
parameter tovsearch dereplicate-sequences
plugin in order to support prefix dereplication.
- @colinbrislawn - Added
- q2-composition
- Reimplemented the volcano plot in
ancom
with Vega. This corrects the bokeh problem we encountered last release. Thanks @thermokarst, @turanoo, and @Nicholas_Bokulich!
- Reimplemented the volcano plot in
- q2-emperor - by @Yoshiki and @Antgonza
- This plugin is now using the latest version of emperor (1.0.0beta17).
- For very large datasets responsive plots can now be rendered live in the browser. Checkout this example with ~114K samples (courtesy of @wasade).
- Fixes a glitch that would happen after re-centering the camera and panning around the scene.
- Adds a new visualizer (
qiime emperor biplot
) to plot the results fromqiime diversity pcoa-biplot
. This method optionally expects feature metadata, this will allow you to modify visual aspects of the Biplot arrows. For an example see this animated GIF:
Happy QIIME-ing!