Uchime Denovo Chimera Filtering Question

Hi everyone,
I apologize for posting so much on this forum, I'm a newbie at bioinformatics and having issues with my MiSeq paired-end data.

I've been having issues with my alpha-rarefaction curve not plateauing despite trying different sampling depths. I've since backtracked and found some adapter contamination and removed those with Trim Galore, but still getting the same rarefaction issues.

Right now, I've been playing around with the Uchime Denovo chimera removal, after using it including the borderline chimeras. If I don't include borderline chimeric sequences, I have very few OTUs.

Can anyone point me in any kind of direction here? The DADA2 filter ends up filtering out all of my sequences so we're trying not to use that (we want both R1 and R2 files).

So far my pipeline looks like this (after importing and merging via vsearch and dereplicating):

qiime vsearch cluster-features-de-novo
--i-table table-native2.qza
--i-sequences rep-seqs-native2.qza
--p-perc-identity 0.97
--o-clustered-table table-trim-97-native2.qza
--o-clustered-sequences rep-seqs-trim-97-native2.qza

#Remove low-abundance OTUs

qiime feature-table filter-features
--i-table table-native2.qza
--p-min-frequency 5
--p-min-samples 3
--o-filtered-table filtered_table-native2.qza

#filter chimeric sequences
qiime vsearch uchime-denovo
--i-table filtered_table-native2.qza
--i-sequences filtered-rep-seqs-native2.qza
--output-dir uchime_output

qiime feature-table filter-features
--i-table filtered_table-native2.qza
--m-metadata-file uchime_output/chimeras.qza
--p-exclude-ids
--o-filtered-table uchime_output/table-nonchimeric-native.qza
qiime feature-table filter-seqs
--i-data filtered-rep-seqs-native2.qza
--m-metadata-file uchime_output/chimeras.qza
--p-exclude-ids
--o-filtered-data uchime_output/rep-seqs-nonchimeric-natives.qza
qiime feature-table summarize
--i-table uchime_output/table-nonchimeric-native.qza
--o-visualization uchime_output/table-nonchimeric-native.qzv

Here is the include borderline chimeras:

Filtering chimeras and borderline chimeras:

An off-topic reply has been merged into an existing topic: Issues finding sampling depth for Rarefaction

Please keep replies on-topic in the future.