Dada2 denoise-pyro for Ion Torrent?

[MiriamGorostidi (Miriam)]

Hello everyone!

I have a really quick question about Dada2. I have read, in more than one post, that dada2 denoise-pyro should be used for Ion Torrent Kit data. However, I don’t understand why… ThermoFisher sequenciation is not performed by Pyrosequencing, but by Ion Semiconductor sequencing. Then, which is the reason of using denoise-pyro for this data?

Thank you in advanced

[thermokarst]

Hi @MiriamGorostidi!

@MiriamGorostidi

Then, which is the reason of using denoise-pyro for this data?

From the DADA2 docs:

Can I use dada2 with my 454 or Ion Torrent data? Yes. We recommend the following parameters for denoising pyrosequencing data (like IT and 454): ...

The denoise-pyro method includes the parameter tweaks suggested by the DADA2 authors. Also note that you should apply a trim-left parameter of 15 when working with IT data, too.

Hope that helps!

[MiriamGorostidi (Miriam)]

Thank you so much @thermokarst