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NCBI Taxonomy IDs for Kraken-Silva Database

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
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updated by lara.h.urban • lara.h.urban • written by josmos43 • josmos43

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

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written by josmos43 • josmos43

2 answers

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.

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written by Asaf Asaf

Asaf : Apologies for high-jacking your answer for a moment but I see that you have started participating regularly on Biostars after a break. You have had moderator privileges on biostars. We have a slack channel for biostars (and some additional closed channels for mods in there). We find it useful to collaborate on moderation issues in the slack channel. Please follow the directions here to join: Inviting NEW Biostars moderators to join Biostars slack channel

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written by GenoMax GenoMax

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?

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written by lara.h.urban • lara.h.urban

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