Alternative methods of read-joining in QIIME 2

No. The reference used by deblur is simply there to identify and remove anything that does appear to be similar to your intended amplicon target (e.g. 16S rRNA). That is, it is intended only to remove spurious artifacts. The deblur denoise-16S uses GreenGenes reference database by default, and cannot be changed. This means any sequence that does not match bacterial or archaeal 16S rRNA gene sequences are discarded. Some 16S rRNA gene primers can amplify 12S & 18S rRNA, or other off-targets. So, these would be mostly removed from your data.

If you are using "universal" primers that are intended to amplify any small sub-unit (i.e. both the 16S and 18S rRNA gene sequences), or simply want to keep these off-targets for further investigation, then you 'd want to make use of the deblur denoise-other. As this will allow you to retain the 18S rRNA sequences, if using SILVA. The denoise-other approach allows you to use any reference sequences, i.e. different 16S rRNA reference databases, (i.e. SILVA, RDP, GTDB), other marker genes, ITS, CO1, etc... for that basic filtering step I mentioned above.

I simply used the example you provided in your original post.

You can make your own 16S rRNA V3V4 region classifier using RESCRIPt. If you do not want to make the classifier yourself you can search the forum for others that have already made a V3V4 classifier. Many are willing to share. :slight_smile: