When are you planning on updating the protein NCBI nr mapping file prot_acc2tax-Nov2016.abin.zip ?
I’ve been rechecking species matches manually using NCBI protein BLAST and finding species level matches more up-to-date than reported using the current mapping file.
The UE uses the same mapping files, however it is bundled with the tools that are used to create the mapping file:
The program MEGAN6UE/tools/ncbi/make-acc2ncbi creates an initial mapping file from data downloaded from NCBI
The program MEGAN6UE/tools/utils/extend-mapping is then used to extend the mapping file by assuming that all accessions that appear on the same header line belong to the same taxon: they are all assigned to t the LCA of all taxa that can be identified for the line.
To run these programs you need to use a server with 100+GB.
I really appreciate your quick response. Analyzing metagenomic samples sometimes feels like hitting a moving target. Having the updated taxonomy mapping file is a big help in keeping up with GenBank updates.