QIIME 1.6.0 is live!

19 12 2012

We’re very excited to announce the QIIME 1.6.0 release, which you can download from here. As usual, we’ll have the updated AWS and VirtualBox images available tomorrow.

Some of the highlights in QIIME 1.6.0 are:

* We’ve updated RDP Classifier re-training support to allow any number of ranks in training files, as long as the number of ranks is uniform. This removes the need for special RDP training files in reference OTU collections. We’ve also posted some tips for defining your own training files.

* assign_taxonomy.py now supports assignment with tax2tree version 1.0 and mothur version 1.25.0.

* Added a new script, compute_core_microbiome.py, which identifies the core OTUs (i.e., those defined in some user-defined percentage of the samples).

* Added a new script, compare_taxa_summaries.py to allow for the graphical and statistical comparison of the taxonomic composition of samples.

* Added a new script, filter_taxa_from_otu_table.py, which allows users to filter OTUs with (or without) specific taxonomy assignments from an OTU table.

* make_distance_boxplots.py and make_distance_comparison_plots.py can now perform Student’s two-sample t-tests to determine whether a pair of boxplots/distributions are significantly different.

* compare_alpha_diversity.py now supports both parametric and nonparametric two sample t-tests (nonparametric is the default).

* Detrending of quadratic curvature in ordination coordinates can now be performed with the new detrend.py script. This is the approach that was used in Figure 3 of Harris JK, et al. “Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.” The ISME Journal (2012).

* Added experimental support for translated database mapping through map_reads_to_reference.py and parallel_map_reads_to_reference.py. This is analogous to closed-reference OTU picking, but translates queries to search against a protein database, so is useful for mapping metagenomic or metatranscriptomic data against databases of functional genes (e.g., IMG). Currently BLAT and usearch are supported for translated searching.

* Added new script load_remote_mapping_file.py and accompanying tutorial to allow exporting and downloading of mapping files stored as Google Spreadsheets. This should be considered experimental (i.e., beta) software at this stage!

* The parallel framework in QIIME has been completely re-written to allow for easier development of new parallel scripts and to facilitate changes to the underlying parallel functionality.

* Building from the recent development of the qiime_test_data repository (as discussed here), which contains example input and output for most QIIME scripts, the script documentation was updated so usage examples correspond to the example input and output files in qiime_test_data. Our script interface testing was greatly improved by this addition as well, which makes the QIIME scripts and documentation more reliable. 

* We replaced add_taxa.py with add_metadata.py to support addition of more general metadata to BIOM files (e.g., OTU tables). add_metadata.py is a script in the biom-format pacakge (a core QIIME dependency). You can find help with add_metadata.py here.

We’ve also re-organized our tutorials page, and added a lot of new tutorials. These include tutorials for predicting mislabeled samplesanalyzing fungal ITS data with QIIMEcomparing taxonomic summaries, loading mapping files from Google Spreadsheets, and analyzing shotgun sequencing data with QIIME (an experimental feature). We’ve also added a new overview tutorial based on analyzing Illumina data which we developed for the ISME 14 QIIME/MG-RAST workshop, rewrote our documentation on parallel QIIME and QIIME parameter files, and expanded our notes on how you can get involved in QIIME development.

So as you can tell, there is a lot packed into this release. You can see a more complete list of changes in our ChangeLog

Enjoy!

Greg, on behalf of the expanding QIIME development group


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