The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.
The NCBI gene calling is too conservative for our needs. As such, Prodigal has been used to call genes on all GenBank and RefSeq genomes. CheckM estimates have already been updated to reflect these new genes. Pfam and TIGRfam annotations should also be recalculated and the GTDB updated to reflect these new annotations (i.e., all existing alignments removed and recalculated).
The NCBI gene calling is too conservative for our needs. As such, Prodigal has been used to call genes on all GenBank and RefSeq genomes. CheckM estimates have already been updated to reflect these new genes. Pfam and TIGRfam annotations should also be recalculated and the GTDB updated to reflect these new annotations (i.e., all existing alignments removed and recalculated).