QIIME 1.1.0 released

15 05 2010

The QIIME development team is excited to announce the latest release of QIIME. You can download QIIME 1.1.0 here.

Some of the new features include:

  • Ability to chimera check sequences with ChimeraSlayer. See identify_chimeric_seqs.py for details.
  • Workflow script for second-stage SRA submission, process_sra_submission.py. The SRA submission tutorial has been extensively updated to reflect the use of this new script. See the SRA submission tutorial document.
  • Added presorting by abundance to the uclust OTU picker. The idea here is that sequences which are more abundant are better representatives when clustering, so they should come first in the file to make them more likely to be used as cluster seeds than less abundant sequences. Also added ability to pass the optimal flag to uclust, which should also improve uclust-picked OTUs, but comes with a performance hit. See the pick otus notes for details.
  • Extensive updates to the alpha rarefaction plotting. This started out as changes to fix an issue with displaying legends which contained long descriptions, but evolved into a complete refactoring of the look and feel of the rarefaction plots. Users can now dynamically switch between metrics and samples, and summary data are included on the same html pages as plots.
  • Added the uclust_ref OTU picker, which uses uclust to pick OTUs against a reference collection. Sequences which are within the similarity threshold to a reference sequnece will cluster to an OTU defined by that reference sequence (similar to the BLAST to reference tree OTU picking protocol), and sequences which are outside of the similarity threshold to any reference sequence will form new OTUs (as in de novo OTU picking). See the pick otus notes for details.
  • Added a 64-bit VirtualBox to support the 64-bit external applications (i.e., sffinfo and sfffile, the Roche 454 off-instrument tools). Users now have a choice between using the 32-bit Virtual Box (mandatory if their system is 32-bit) or the 64-bit VirtualBox. Get details on the QIIME Virtual Box here.

QIIME 1.1.0 still relies on PyCogent 1.4.1 and PyNAST 1.1, so no dependency changes from QIIME 1.0.0 there. The only external dependency version change is with Denoiser: users will need to upgrade to Denoiser 0.84 to denoise 454 data with QIIME 1.1.0.

As always, get in touch with qiime.help@colorado.edu if you run into any questions.

Thanks, and good luck!

Greg

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