Greengenes 13_5

20 05 2013

The Greengenes Consortium is pleased to announce the release of Greengenes 13_5, expanding our coverage of the Archaea and Bacteria to 1,262,986 sequences with 203,452 99% OTUs and 99,322 97% OTUs. You can find the files for this release on the official Greengenes 13_5 database page.

This new release comes with a few backend changes:

* The ARB database (to be released a few days behind this official release) will include sequences as aligned by PyNAST v1.1 (Caporaso et al 2010) and are safe for probe design. Thanks to Les Dethlefsen for contacting us about this.

* Alignments from SSU-Align (Nawrocki 2009) and PyNAST (Caporaso et al 2011) are now provided. The de novo tree used by Greengenes is based on the SSU-Align alignment but we are now providing the PyNAST sequences for completeness.

* Chimera checking is now only performed using UCHIME (Edgar et al. 2011). As with the last release, the reference database used was comprised of the consensus sequences from the 94% OTUs the previous release (GG 12_10 in this case). Previously flagged chimeras are still excluded.

* Mappings to the Integrated Microbial Genomes database are now included.

* The inference for determining whether a record is a named isolate or clone has been revamped.

* An outline of the taxonomy changes is included that describes the taxonomic name change, the number of affected tips, and an example identifier that can be traced back to the tree.

The top 5 major group changes are:

Screen Shot 2013-05-20 at 3.12.08 PM

Suggestions and improvements to the taxonomy were made by a collection of people. We’d like to thank Alex Probst, Bing Ma, Francesca DeFilippis, Kyle Bittinger, Niels Larsen and Cathy Lozupone for their feedback. Greengenes is a living project, and the feedback we receive is vital for improving the utility of this resource.

The Greengenes Consortium is composed of the University of Colorado, Second Genome, and the University of Queensland.

We look forward to hearing your feedback!

– Daniel McDonald (on behalf of the Consortium)

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