taxonomy files for common 16S datasets?

[faylward]

Thank you for creating this tool - it is extremely useful!
I have been using some of the Kraken2 16S databases that are pre-compiled (RDP, SILVA, etc), and unfortunately these outputs are not compatible with recentrifuge because they do not use the NCBI taxonomy. Do you have any suggestions for using recentrifuge with analyses that have been done on 16S reference databases?

[khyox]

Good question and sorry for the delay in addressing it! Recentrifuge is build to support any ontology even beyond taxonomy —in fact, Recentrifuge v2.0.0 shows this as rgf supports functional metagenomics when provided by a special graph-to-tree Gene Ontoloy. So, you can derive any taxonomy from the Ontology class. If you have an equivalent to the NCBI Taxonomy nodes.dmp and names.dmp things would be even easier.