The QIIME 2 2023.2 release is now available! Thanks to everyone involved for their hard work!
As a reminder, our next planned QIIME 2 release is scheduled for May 2023 (QIIME 2 2023.5), but please stay tuned for updates.
Check out the QIIME 2 2023.2 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!
Docker images have been built and are ready for use!
Here are the highlights of the release:
@lizgehret fixed a in ANCOM-BC where a
reference_levelvalue was chosen that is a column within the metadata, but the associated IDs from that group are not found in the feature table No error would be raised, ANCOM-BC just defaulted back to alphabetical order for the intercept column
This will now produce an error that includes the
reference_levelvalue, along with the IDs not found in the table
@lizgehret added type enforcement for the
reference_levelparameter, which now only allows numerical metadata columns to be used
- @lizgehret added citations for ANCOM and ANCOM-BC methods
@lizgehret made some improvements to the
- Each tab now contains the data slice name and short descriptions for LFC and W-Scores
- Columns used to calculate the intercept are included at the top of each slice's table
@gregcaporaso added a new visualizer called
da_barplotthat adds support for generating bar plots from ANCOM-BC data, inspired by Figure 6 in the ANCOM-BC paper
@crusher083 added a new flag in ANCOM called
--filter-missingthat will filter samples with missing metadata when enabled, and will produce an error that includes the IDs with missing metadata if disabled
- @lizgehret fixed a in ANCOM-BC where a
ghubrakesh authored a change that makes the language used for the
summarizeoutput more clear, changing feature count to frequency
- ghubrakesh authored a change that makes the language used for the
@cherman2 added a Proportional Engraftment of Donor Strains(PEDS) method called
sample_pedsthat tracks percentage of donor features that were transferred to the recipient after FMT intervention The method is further explained in Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes | Nature Microbiology.
@cherman2 added a new visualizer called
plot_heatmapthat adds support for generating a heatmap to visualize PEDS for each subject over time
- @cherman2 added a Proportional Engraftment of Donor Strains(PEDS) method called
@lizgehret fixed some and associated test failures caused by API changes to the
- @lizgehret fixed some and associated test failures caused by API changes to the
@colinbrislawn made a small update within the
per_sample_sequencesformats that updates the call of
.items, since pandas will be deprecating
.iteritemsin the near future
- @colinbrislawn made a small update within the
- @wasade revised the Greengenes entries to now include 2022.10, which is the latest release of Greengenes2