Denoising IonTorrent data with dada2

[Matjaz]

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

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

Thank you.
Best,
Matjaž

[thermokarst (Matthew Ryan Dillon)]

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!

[Matjaz]

Thank you very much for your help.
Best,
Matjaž