We’re very excited to announce the QIIME 1.7.0 release. This includes tons of new features and documentation updates, so lots of new stuff to play with!
The biggest highlights are listed below, but for the adventurous you can view this awesome list of all of the QIIME commits.
Changes in QIIME 1.7.0 include:
* Preliminary (beta-level) support for integration with the Galaxy Framework. Using the new QIIME-Galaxy integration utility, you will be able to run QIIME within Galaxy, taking advantage of the Galaxy GUI.
* The core_qiime_analyses.py script has been replaced with the new core_diversity_analyses.py. This is a complete refactoring to support only “downstream” analyses (i.e., starting with a BIOM table). We’ve found that this makes the script more widely applicable as it’s now general to any BIOM data and/or different OTU picking strategies. See issues #477 and #688 for details.
* The three main OTU picking workflows, pick_otus_through_otu_table.py, pick_reference_otus_through_otu_table.py, and pick_subsampled_reference_otus_through_otu_table.py have been renamed for clarity to pick_de_novo_otus.py, pick_closed_reference_otus.py, and pick_open_reference_otus.py, respectively. We have additionally created a new OTU picking document that describes the differences between these OTU picking protocols, and illustrates how to use each one. See issue #708 for more details on this. These updates include support for usearch 6, which is not available publicly yet, but due out soon.
* New documentation on working with BIOM tables in QIIME, using state strings to select certain samples that should be included in analyses, and tracking the source of microbial communities using SourceTracker.
* Under the hood, we’ve completely refactored the QIIME workflow framework to support easier development of QIIME workflow scripts in the future. We’ve also merged the qiime_test_data repository into QIIME, which facilitates our testing efforts.
* The per_library_stats.py script has been removed in favor of biom-format’s print_biom_table_summary.py, which provides additional information on top of per_library_stats.py.
* summarize_taxa.py now outputs taxa summary tables in both classic (TSV) and BIOM formats by default. This will allow taxa summary tables to be used with other QIIME scripts that expect BIOM files as input, including core_diversity_analyses.py and many of the scripts discussed here.
* We found and fixed a bug in the creation of biplots using make_3d_plots.py. This bug would change the placement of taxonomic groups based on how many taxa were included in the biplot analysis (the default was 10). Based on several tests that we ran, this did not effect biological conclusions that would be drawn from the data, but we suggest rerunning to verify that this is the case in your biplots. For more details and a more in-depth explanation see issue #677.
Finally, due to the ever-increasing number of samples and amount of metadata in studies of microbial ecology, we’re very excited to announce a new software package, Emperor, which we plan to use as a replacement for KiNG for viewing 3D plots in QIIME 1.8.0. This is a new WebGL, non-Java, Chrome-specific, visualization tool that scales much better than KiNG. This is now available as beta software, if you’d like to try it out. You can see details on the features in its ChangeLog. We encourage QIIME users to test this new tool and add suggestions and report bugs in the Emperor issue tracker.
Enjoy QIIME 1.7.0! This is only a partial list of the changes – you can view the full ChangeLog with further detail here. As always, get in touch on the QIIME Forum with any questions, and submit Pull Requests with any contributions.
We hope to see you at ASM next week!
Greg (with help from Antonio, Jose, Yoshiki and Jai), on behalf of the ever-growing QIIME development group