QIIME 1.3.0 is live!

29 06 2011

We’re proud to announce the release of QIIME 1.3.0 today! Some important things to know about the upgrade are listed on the new “Upgrading …” page. Go here for instructions on how to upgrade existing installations of the QIIME VB. For AWS users, the QIIME 1.3.0 EC2 image identifier is ami-dce51eb5.

This a major release of QIIME, packed with too many new features to cover them all here. Some highlights are:

* Added support for the RDP Classifier version 2.2 in response to several feature requests. QIIME now supports RDP 2.0 and RDP 2.2.

* Overhauled support for Illumina data in QIIME with a new script, split_libraries_fastq.py. fastq is now the default format for incoming Illumina data to QIIME, and several scripts have been provided to convert other file formats to fastq (process_qseq.py and process_iseq.py). Check out the “Processing Illumina Data” tutorial for an overview of how to work with Illumina data in QIIME.

* Full integration of the QIIME Denoiser (Reeder and Knight, 2010) into Qiime: Denoiser is no longer a stand-alone package. Some enhancements were made to the Denoiser in the process, including check-pointing for failure recovery.

* Added support for AmpliconNoise via the ampliconnoise.py script. We’ve also dropped support for PyroNoise as AmpliconNoise is the successor to that package.

* Added the core_qiime_analyses.py script. This plugs together many components of QIIME (split libraries.py, pick_otus_through_otu_table.py, beta_diversity_through_plots.py, alpha_rarefaction.py, and several others) in an effort to combine the core functionality in a single command. The output of this script includes an html page that serves as an index into the results, to facilitate sharing of results. This script should be considered to be in BETA status. One known issue is no failure recovery – if an analysis fails at some point in the analysis it’s not possible to continue where the failed run left off, possibly resulting in wasted compute time.

* Parameter files have been made optional for all workflow scripts. This greatly simplifies the interface for the workflow scripts when users want to work with default parameters.

* Added the plot_taxa_summary.py workflow script, which includes (optionally) summarizing the OTU table by category, then summarizing taxa for an OTU table, and generating area, bar, and pie charts.

* A lot of updated and new documentation: the QIIME Overview tutorial, the Illumina data processing tutorial, and the Denoiser tutorial have all been overhauled, and a new tutorial has been added that covers processing 18S data with QIIME. A lot of minor documentation changes have been pushed in through-out the code base.

* The beta_diversity_through_3d_plots.py has been renamed to beta_diversity_through_plots.py to reflect additional functionality. It now also generates 2d plots and distance histograms, and any of the plots can be disabled by passing the options –suppress_distance_histograms, –suppress_2d_plots, and –suppress_3d_plots.

* Added inflate_denoiser_output.py script to simplify the integration of denoiser results into the QIIME pipeline. See the Denoiser tutorial for details. To reduce the number of possible pathways through QIIME with denoising (which were difficult to support), support for denoising was removed from pick_otus_through_otu_table.py in favor of working with the pipeline presented in the tutorial.

* Reorganized and renamed output from the workflow scripts for clarity. You’ll notice changes in your results from pick_otus_through_otu_tables.py, pick_reference_otus_through_otu_tables.py, and beta_diversity_through_plots.py. The same files are still created, but with less complex naming of files and a simpler directory structure.

* Added plot_semivariogram.py to plot semivariograms using two distance matrices.

* Added filter_tree.py which prunes a list of tips from a tree. Lists of tips can be provided in similar ways as to filter_fasta.py.

* Added make_tep.py, which creates a TopiaryExplorer project file (.tep) from an otu table, a metadata mapping file, and a tree.

* We’ve posted help videos for getting setup with the QIIME VirtualBox and EC2 which you can find here.

Check out the ChangeLog for a more comprehensive list of the changes in QIIME 1.3.0.

A few additional notes:

* For QIIME VB users: we now recommend making at least 2GB of RAM available to your VirtualBox.

* We’d like to thank Paul Marshall for his work on the app_deploy.py script. This is a very useful tool for installing/upgrading QIIME (and other software) in Linux environments, and was used for building the QIIME 1.3.0 VirtualBox and EC2 instances. It is available for our users to upgrade/install QIIME, but should be considered to be in BETA status – this has been tested in the QIIME VirtualBox, but is not recommended for use on production systems at this stage.

* Due to popular demand, we’ll be adding a page soon that lists courses and workshops that will cover QIIME. We’ll post to the blog when that page goes live.

Thanks to all of the QIIME developers for the hard work that went into QIIME 1.3.0, and to our users for all the feedback that helps us improve QIIME. As always, get in touch on the forums if you run into questions. Have fun!

-Greg

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