DADA2 and Deblur outputs are extremely different

[SoilRotifer (Mike Robeson)]

@Stephan_Bitterwolf

Perhaps there is a way for me to add the missing sequence to SILVA? The sequence can be found on GenBank

Yes there is. You should be able to follow one of these tutorials:

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt - #7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Benj…

From here you should be able to run qiime feature-table merge-taxa... and qiime feature-table merge-seqs ... to combine the GenBank and SILVA data.

Note that, prior to merging, there is a chance you'd have to run qiime rescript edit-taxonomy ... on the fetched NCBI taxonomy data to change the k__ prefixes to d__, so that it matches SILVA. Assuming you are downloading the standard 7 ranks (kpcofgs). Otherwise you'll have to do more editing.