********* Changelog ********* Greengenes 12_8 - 12_10 ======================= New Features ------------ Changes ------- Bug Fixes --------- * Right before officially posting the 12_8 release, we discovered a flaw in the OTUs affecting the full release. Specifically, the OTUs were picked off of masked sequences. The resulting OTUs were not incorrect, but their specificity was reduced. Thank you to Greg Caporaso for discovering the issue. The 12_10 release is effectively a bug fix. On the plus side, we were able to put additional effort in on curation. Greengenes T2T - 12_8 ===================== New Features ------------ * Workflow tools refactored to work towards standarized releases * Chimera checking now uses Bellerophon and Chimera Slayer targeting gross chimeras * Various deliverables now available, please see 00README * Taxon names, in particular candidate phyla, are sync'd with Silva Changes ------- * prokMSA_id has been depreceated in preparation for supporing 18S sequences. The analogous field is known as GG_ID. If a sequence previously had a prokMSA_id, it was retained as its corresponding GG_ID * Additional fields are now tracked in the Greengenes records, including chimeric information. * Taxonomy decoration is based off of the 99% OTU tree * The Greengenes source code is now under the GPL and available from https://github.com/greengenes/Greengenes. NOTE: this code does not yet provide the full workflow and is an active development project * Greengenes is now controlled by the Greengenes Consortium represented by individuals at the BioFrontiers Institute at CU-Boulder in the USA, the Australian Centre for Ecogenomics at the University of Brisbane in Australia and Second Genome in the USA. Bug Fixes --------- * The percent invariant filter is now being used. The previous release did not drop sequences that varied against known invariant positions resulting in incorrect grouping within the topology.