Classifier Silva 138 99% OTUs full-length sequences with sklearn version 1.4.2
New taxonomy, a little better:
taxonomy-full-silva.qzv (734.1 KB)
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Continues with approx 25% unassigned.
Should I do anything else to remove that.
You are limited by data quality affecting the merges. Thus, there is not much you can do about that.
I still strongly suggest you compare this output to those processed using only the forward reads. Even with only forward reads, can still reliably identify the microbes, and have much more data to boot! That is, there is a chance that you are losing information about the microbial community as a result of a technical artifact... tossing out a lot of data that fails to merge.
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