Difference between single-end and pyrosequencing processing?

I have been processing all single-ended sequences using denoise-single. I understand that pyrosequencing is a different sequencing technique than standard methods, but what differences would I expect by processing pyrosequenced sequences as normal single-end?

Hi @michaelsilverstein, have you seen this FAQ about pyrosequencing, on the DADA2 website?

https://benjjneb.github.io/dada2/faq.html#can-i-use-dada2-with-my-454-or-ion-torrent-data

Hopefully that helps answer any questions (if you haven’t spent much time reading the DADA2 docs, I suggest you catch up there, too!).

Hey Matthew,

Thanks for the response. I took a look at the DADA2 documentation, but I’m still confused about the difference between denoise-pyro and denoise-single.

Is it just that the HOMOPOLYMER_GAP_PENALTY and BAND_SIZE arguments are internally set as suggested by the DADA2 documentation?

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Yes indeed! Behind the scenes both methods run the same code, just with the adjusted internal parameters tweaked. Hope that helps!

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