I can only find the newest silva as an “arb” file. Does anyone know how I can use this in Mothur?
Pat answered me the v138 will be formatted for Mothur by the end of last month, I sent him a private message yesterday as my post is closed, let0s see what he says! hope the new version is released soon
Firstly, thanks Pat & team for the new SILVA mothur version!
Secondly, just in case somebody is interested: The mothur WIKI states for the new SILVA reference files regarding the SSU Ref NR 99 database that “It’s unclear why this version of the release is smaller than previous releases.”
The reason for this is a change in the use of the clustering algorithm from uclust to vsearch which, while reducing the number of clusters/sequences, gives according to the SILVA team (I asked them ) a more robust result that still retains all branches of the previous version. The SILVA people will also add an explanation to their webpage about this.
Thanks, Rene! I also want to underscore that this version is available under the CC-BY license, which means people working in for-profit institutions are welcome to use it. Yippee for open science!
Thanks for the update!
I checked the v138 formatting for mother earlier and found that there are some corrections that are not required for this version anymore. It’s just a minor thing since it doesn’t do any harm but I’ll leave it here anyway and maybe you want to remove these from the formatting description.
The commands mentioned are all in the “formatting the taxonomy files” section:
- RsaHf231 is now included although not at the phylum level:
map.in <- rbind(map.in, c("Bacteria;RsaHf231;", "phylum")) #wasn't in tax_slv_ssu_138.txt
- Not sure exactly, why this was there but it doesn’t do anything:
#fix Escherichia nonsense map.in$taxlevel[which(map.in$taxlabel=="Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;")] <- "genus"
- Polaribacter is OK in v138:
# Following line corrects the Bacteria;Bacteroidetes;Bacteroidia;Flavobacteriales;Flavobacteriaceae;Polaribacter;Polaribacter; problem tax.in$taxlabel <- gsub("Polaribacter;Polaribacter;", "Polaribacter;", tax.in$taxlabel)