DADA2, truncation lengths and features number

Minimum overlap is 20 nts for merging, but you need to factor in some biological length variation in the amplicon size as well, so I'd say at least 30nts of overlap for V3/V4.

Not just acceptable, usually the right choice. Here the reverse reads are clearly worse quality, so should be truncated earlier than the forward reads. Perhaps trunc-len-f 280 and trunc-len-r 220? That gives 500 total nts after truncation, so still safely overlapping, and gets rid of the worst quality region.

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