I am trying to run Kraken2 on 16S data, using the Kraken2-Silva database (built with "kraken2-built --special silva). The taxonomic IDs listed in column 5 of the kraken report does not correspond to the NCBI Taxonomy. (I need the correct IDs to visualize the results with Krona)
I am trying to find a way to map the NCBI IDs to the SILVA IDs. I found some mappings on the Megan6 page but it does not resolve the taxonomic IDs for the lowest common ancestors (higher ranks).
I would appreciate any Ideas how to go about this issue. Ideally, I would like to replace the Taxonomic IDs in the Files the Kraken database is built with.
Maybe there is also a way to create the Krona-plot for Kraken-output without Tax-IDs (ktImportText instead of ktImportTaxonomy)?