uclust bug fix, OTU and taxonomy files, and (coming soon) QIIME 1.2.0

29 10 2010

A few important QIIME-related notes:

Bug in reference-based uclust (i.e., uclust_ref)

Most importantly, we identified an issue with uclust that resulted in some sequences being lost when picking OTUs against a reference set with the serial version of uclust_ref, when allowing for new clusters and there are greater than 100k seeds. The call that would possibly have been affected is pick_otus.py -m uclust_ref; but not parallel_pick_otus_uclust_ref.py;  pick_otus.py -m uclust; or pick_otus.py -m uclust_ref –suppress_new_clusters.

If you suspect that a run may have been affected, get in touch on the QIIME forum and we’ll give you a script to check your OTU map. A new version of uclust has been posted to fix this, and as of QIIME 1.2.0 (and the current svn version) this will be the minimum supported version of uclust. Here are links to the uclust 1.2.21q binaries. You should install this ASAP.

QIIME-compatible Greengenes files

Next, we’re excited to announce that Greengenes is now hosting QIIME-compatible reference sequences and taxonomy files. These are frequently requested for use with QIIME’s BLAST taxon assigner (they get passed as  -r and -t, respectively). The reference file is based on 97% OTUs that we picked from greengenes. This is also useful for reference-based OTU picking (e.g., with uclust_ref or blast), in which case the included tree can be used in phylogenetic diversity calculations. Our 6oct2010 build of the greengenes OTUs is available here, and additional notes on that build are available here.

Coming soon: QIIME 1.2.0

Finally, we’re about to make the push toward QIIME 1.2.0, which we hope to release within the first couple of weeks in November. We’ll be releasing a new VB image, but also providing an upgrade script for existing VB users so you won’t have to start fresh with a new VB image if you don’t want to. There are lots of exciting changes coming in 1.2.0 — more on that soon.

-Greg

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