Quality score and trimming in Dada2

One addition to that: You need to have 20 y's, plus enough additional y's to handle the biological length variation in your amplicon. If you aim for the minimum, you will lose real variants that are a few nts shorter than the average amplicon length, and therefore systematically drop certain taxonomic groups.

20 is the bare minimum, but err on having more overlap. If you can get an overlap of 80 with acceptable quality, I would go for it.

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