Pretty sure this doc covers just about all you’d need for basic filtering. You might want to filter both the feature table as well as the sequences if you’re removing samples though. As @Nicholas_Bokulich pointed out in a recent question of mine, you can do this by filtering (dropping) the samples you want with the filter-features argument in QIIME, then using that filtered table to then create an updated sequence set based on inputting that filtered feature table.
Hope that answers your question.
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