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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Formatting RDP version 19 taxonomic database for DADA2 #2014

Open jheiman06 opened 2 months ago

jheiman06 commented 2 months ago

I am working on processing bacterial 16S rRNA sequences with DADA2. I would like to classify these sequences with the newest update of the RDP database (version 19), but I have yet to find it formatted for DADA2. I have found the code to format it myself, and this was successful for the "assignTaxonomy" function, but I have not been able to format the species file correctly. I think this is because I cannot find the unaligned bacteria file as the RDP site at Michigan State is no longer working. Has this database (RDP version 19) been formatted for DADA2? If not, do you know where I could find the unaligned bacteria file in order to format the species file correctly?

benjjneb commented 2 months ago

Has this database (RDP version 19) been formatted for DADA2?

Nope, on the to-do list now though.

If not, do you know where I could find the unaligned bacteria file in order to format the species file correctly?

Not sure, but I will look into this more later this month.

nvwinsen commented 2 weeks ago

Is it possible to format the RDP v19 database including species instead of a separate species table? This way bootstrapping can be included for species with RDP (which now is only possible with Silva).