QIIME 1.2.1 is live!

23 02 2011

We are happy to announce a minor QIIME release today: QIIME 1.2.1.

Some of the notable new features are:

  • In response to NCBI’s announcement to drop support for SRA, we no longer support submission of data to the SRA using QIIME. We now support submission of data to MG-RAST using the new submit_to_mgrast.py script.
  • The make_pie_charts.py script has been replaced with a new script, plot_taxa_summary.py, which in addition to creating pie charts will also create area charts and bar charts. These new plots are particularly useful for looking at how taxonomy changes across time/space gradients. We’ve created a new taxa summary tutorial showing how to use this new script. You can find some example bar plots there.
  • Added binary_otu_gain as a new beta diversity metric to compute non-phylogenetic gain (G), or the amount of new OTUs in a sample (or samples) with respect to another sample (or samples). This complements the phylogenetic variant of this metric, unifrac_g.
  • Added a reference-based OTU picking workflow script, pick_reference_otus_through_otu_table.py, which performs strict reference-based OTU picking where a pre-existing tree and taxonomy will be used (allowing users to bypass the slow steps where these are created in the pick_otus_through_otu_table.py workflow). This can also be used for applying the Shotgun UniFrac pipeline.
  • Changed defaults for uclust and uclust_ref OTU pickers, as described in this blog post.
  • Added support for generating inVUE plots in make_3d_plots.py.
  • Changed the method for p-value calculation in Procrustes analysis Monte Carlo in response to SF bug # 3189200.

As of QIIME 1.2.1, we moved the EC2 image out of beta testing status, and have now released it as an EBS which means that it is possible to save the state of the machine and (manually) pause it to save money when not actively running jobs. We encourage users to try this out as our initial uses of this have been very successful. This is a great way to get a lot of compute power, relatively cheaply, for your QIIME runs. Information on running QIIME on EC2 is here. You can find the official image by searching for AMI ami-0c12e165. After booting the image in your own amazon account, you’ll then log in as user ‘ubuntu’.

Updated versions of the QIIME VirtualBox and the EC2 image are now available, as is a new version of the QIIME VirtualBox update script. We recommend updating to the latest version of the Oracle VirtualBox software as they seem to have fixed some issues that were present in the previous versions.

Also note that we’ll be maintaining links to the most recent versions of dependencies, as well as our most recent build of the Greengenes references OTUs on the top right corner of the blog homepage so you can always find that information there.

Have fun!

Greg

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