Thanks for investing the time to convert the mapping DB files to SQLite files - it makes them very accessible.
I have a question about customizing the mapping db files for a particular use-case:
Is it possible to include a custom mapping entry for an organism that is not currently present in the NCBI taxonomy?
For example, let’s say we have a specific strain of species X (or a new species Y), and we would like that to show up in MEGAN. I can certainly make up a unique “accession” number for the sequences in the reference database used, and also add those to the mapping db. However, what should be used for the taxonomy ID in the mapping db? The taxonomy ID number for species X would not be ideal, because we would like to distinguish this “new” organism from species X. Similarly, if there is no entry for species Y, is there a possible workaround to allow some type of taxonomic labeling?
Any advice would be greatly appreciated!