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?
