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I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found Krona uses NCBI taxonomy as its default. Krona github page has the following instruction regarding RDP database:

Taxonomic classifications of the Ribosomal Database Project 16S Classifier can be imported using ktImportRDP. To download classifications:

Run the classification tool.

Click "show assignment detail" for the root of the hierarchy.

Click "download allrank result" or "download fixrank result".

Problem is the online RDP classifier (http://rdp.cme.msu.edu/classifier/classifier.jsp) doesn't work and as far as I understood the above mentioned help applies only for web version of the tool.

And for Greengenes taxonomy id file found here , it is in different format than the one Krona uses. Krona taxonomy file looks like this:

1   0   1   no rank root
2   2   131567  superkingdom    Bacteria
6   7   335928  genus   Azorhizobium
7   8   6   species Azorhizobium caulinodans
9   8   32199   species Buchnera aphidicola
10  7   1706371 genus   Cellvibrio
11  9   1707    species Cellulomonas gilvus
13  7   203488  genus   Dictyoglomus
14  8   13  species Dictyoglomus thermophilum
16  7   32011   genus   Methylophilus
17  8   16  species Methylophilus methylotrophus
18  8   213421  genus   Pelobacter
19  9   18  species Pelobacter carbinolicus
20  7   76892   genus   Phenylobacterium
21  8   20  species Phenylobacterium immobile
....

And Greengenes taxonomy file mentioned above looks like following:

228054  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
844608  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
178780  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
198479  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
187280  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
179180  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
175058  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
176884  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synechococcales; f__Synechococcaceae; g__Synechococcus; s__
228057  k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__Pelagibacteraceae; g__; s__

I am stuck here. Where can I find taxonomy databases that use the format Krona uses? Is there any tool I can use to convert between these formats?

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  • $\begingroup$ Same problem here! $\endgroup$
    – 5norre
    Mar 24, 2022 at 13:25

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