NCBI Taxonomy IDs for Kraken-Silva Database

Question

[josmos43]

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)?

[josmos43]

I solved the issue buy using "ktImportText" instead, creating the text file from the kraken report

Answer 1

[Asaf]

You should have the NCBI taxonomy ID in the kraken2 database folder under the file seqid2taxid.map . Can you post some examples for the output? I suspect you got taxonomy IDs but perhaps not in the desired level.

Answer 2

[lara.h.urban]

The names.dmp file in the taxonomy folder of the kraken2 database folder contains the mapping of the SILVA IDs to the bacterial names; perhaps this helps?