Question: NCBI Taxonomy IDs for Kraken-Silva Database
gravatar for josmos43
22 months ago by
josmos430 wrote:

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)?

rna-seq • 1.2k views
ADD COMMENTlink modified 17 months ago by lara.h.urban0 • written 22 months ago by josmos430

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

ADD REPLYlink written 20 months ago by josmos430
gravatar for Asaf
22 months ago by
Asaf8.4k wrote:

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

ADD COMMENTlink written 22 months ago by Asaf8.4k
gravatar for lara.h.urban
17 months ago by
lara.h.urban0 wrote:

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?

ADD COMMENTlink written 17 months ago by lara.h.urban0
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