How to map taxonomy assigned using SILVA database to NCBI ID (preferably in R)?
I'm using R Dada2 and SILVA database to assign taxonomy: Bacteria > Firmicutes > Bacilli > Lactobacillales > Enterococcaceae > Enterococcus
I need to map it to NCBI ID: 2 > 1239 > 91061 > 186826 > 81852 > 1350
Or at least use lowest rank to get NCBI ID: Enterococcus > 1350
I see tool such as Crossclasify (and related paper from Monika Balvočiūtė), but DBs over there are quite old (SILVA 128). Any alternative? Is there any map that can be easily used?