Denoising IonTorrent data with dada2

User Support
1

Dear All,
I'm new to metabarcoding field and QIIME 2 as well. I've gone through the tutorials and I would like to praise you for a very well written instructions. I would like to analyse IonTorrent data and I noticed in dada2 instructions that the following parameters are recommened in this case
dada(..., HOMOPOLYMER_GAP_PENALTY=-1, BAND_SIZE=32)
filterAndTrim(..., trimLeft=15)
source: Frequently Asked Questions

Is it possible to use the first two parameters ("homopolymer gap penalty" and "band size") in dada2, integrated in qiime2?

Thank you.
Best,
Matjaž

3

Hey hey @Matjaz!

Have you had a chance to look at the denoise-pyro command in q2-dada2? This method is tuned to apply those HOMOPOLYMER_GAP_PENALTY and BAND_SIZE settings, already! As well, it exposes a p-trim-left parameter that you could then set to 15.

Let us know how it goes! :fire: :fire: :fire:

:qiime2:

5

Thank you very much for your help.
Best,
Matjaž

6

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