Most similar DADA2 taxonomic reference to ChocoPhlAn


We are currently planning to re-process some 16S rRNA amplicon sequences using updated DADA2 version and reference databases (it’s been a few years, so it’s time to update our taxonomic assignments). In addition to our 16S data, we also have some new shotgun metagenomic sequencing data that we have processed using HUMAnN/MetaPhlAn 3 with the most up to date ChocoPhlAn release (v296_201901). We would like to have both 16S and shotgun taxonomic assignments as similar as possible (barring obvious differences between 16S and shotgun taxonomic assignment). What 16S taxonomic reference database would be recommended to use with DADA2 to achieve this (i.e. what 16S taxonomic reference database is most similar to ChocoPhlAn)?

Thank you for your help,

For some clarification, an educated opinion, or speculation, on the topic would be sufficient… I am definitely not requesting a recommendation based on a tested assessment of which 16S databases are most similar to ChocoPhlAn.

Hi Zach,
Sorry for not catching this earlier. I would choose the SILVA database, the releases come with a mapping file that associates the SILVA taxonomy with the NCBI one (the one used by ChocoPhlAn) (Archive).