QIIME 0.92 released!

5 03 2010

The QIIME development team has released QIIME 0.92 today, marking the second stable release of the QIIME package.

The major changes to QIIME are the new documentation (which is now live at http://qiime.sourceforge.net) and the release of the QIIME virtual box.

The QIIME documentation is now packaged as restructured text files with QIIME in Qiime/doc and subdirectories. We use Sphinx to generate the html for the web-based documentation. For users of the stable QIIME releases, the web-based documentation will always be in sync with the latest QIIME release. For svn users, the svn documentation will remain as close as possible to the svn version of the code. (svn users should see the README in Qiime/doc for instructions on how to build the html locally.)

The QIIME virtual box is a full Ubuntu Linux virtual machine image that can be used with Sun’s Virtual Box software. This virtual machine contains all of QIIME’s optional and required dependencies (except for sff tools, which we legally cannot include), and is a fully functional QIIME installation. This should greatly ease the install process for less advanced users, and provides full access to QIIME data analysis and visualization capabilities. The QIIME virtual box should also be useful for new users to evaluate QIIME before installing it natively on their systems.

Some additional changes in QIIME 1.0 are a new uclust-based OTU picker; workflow scripts for chaining together individual steps of the QIIME pipeline (for example, see Qiime/scripts/jackknifed_upgma.py); cleaner and more standardized command line interfaces; and bug fixes and many other enhancements through-out the code base. You can see a detailed list of the changes in Qiime/ChangeLog.

There are two important interfaces change to note between Qiime-0.9 and Qiime-0.92. First, if you were previously calling Qiime scripts from Qiime/qiime (e.g., Qiime/qiime/align_seqs.py -h) you’ll now need to call those scripts from Qiime/scripts (e.g., Qiime/scripts/align_seqs.py -h). Second, the rarefaction.py script was split into two separate scripts: single_rarefaction.py, for building a single rarefied OTU table at a given sampling depth; and multiple_rarefactions.py, for building multiple rarefied OTU tables at a range of sampling depths. Your calls to rarefaction.py will need to be modified to refer to the correct one of these two scripts.

If you run into any questions with the release, as always feel free to e-mail Qiime Help.

Finally, thanks to all of our users for the valuable feedback that helped us improve QIIME for this release! Your input continues to be extremely valuable to us as we roll toward QIIME 1.0.

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