Greengenes Database（16S）

The Greengenes Database Release 13_5

Greengenes is operated and maintained by an international consortium, The Greengenes Database Consortium, representing academic and biotech interests. Many improvements and changes have been made to the process by which the database is built in an effort to streamline the release cycle. For this release, a few major changes have been made:

1. Chimera detection now relies on UCHIME (Edgar 2011) using, as a reference, consensus sequences derived from the 94% OTUs from Greengenes 12_10. Previously identified chimeras are still considered chimeric.
2. The inference for determining if a record named_isolate, unnamed_isolate, or clone has been dramatically improved. All existing Greengenes records have been updated and now reflect the improved decision status.
3. Mappings to the Integrated Microbial Genomes databas v400 are now provided. See gg_13_5_img.txt for a mapping between the Greengenes ID and IMG genomes.
4. PyNAST aligned sequences are now provided, and are included in the ARB database. Thank you Les Dethlefsen for pointing out the need for these.
5. Taxon names above the rank of genus种 with square brackets are names proposed by the greengenes curators and will not be found in NCBI. Genus names with square brackets are contested names (usually due to polyphyly of the genus) some of which will be found in NCBI.

Source code. Parts of the Greengenes code base are provided here: https://github.com/greengenes/Greengenes However, the provided code is still quite limited. We're continuing to make changes on the backend of Greengenes, and the structure of the code base has not yet finalized.