DADA2 prep question - Trimming more or lowering quality score cut offs. The sweet spot?

To add one thing to what @ebolyen said: The key thing with the amount of overlap to keep, is that it must be at least 20nts + the natural length variation of the amplicon. (Warning: made up numbers ahead). For example, if the average V3-V4 amplicon is 460nts, but can naturally be as short as 450nts, then you need 20nts+10nts of overlap (in the average case) to maintain 20nts of overlap in the case of the shortest natural amplicons.

As long as you have that minimum amount of overlap, its usually better to truncate off sequence tails after the quality has crashed (if it does).

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