priors in qiime2-dada2

General Discussion
1

Hi,
is there an option in the dada2 plugin under qiime2 for "priors" specific sequences as reported in the dada2 tutorial for pseudo-pooling?
https://benjjneb.github.io/dada2/pseudo.html

2

Hello Alberto,

Welcome to the forums! :qiime2:

You can sort of do this within the Qiime2 pipeline.
https://docs.qiime2.org/2023.2/plugins/available/dada2/denoise-paired/

While you can't provide expected sequences, you can use
--p-pooling-method pseudo
to enable pseudo-pooling, which uses sequences from other samples in your input when inferring reads in each sample.

You may have noticed this already, but in general, using the software directly gives more more options and control, while the Qiime2 plugin gives you good defaults and a streamlined pipeline with some of the settings exposed. 'DIY' vs 'Just Works'

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3

Thank you Colin for the reply! I was indeed already using the option

--p-pooling-method pseudo

but the sequences i spiked in in my samples resulted in a big number of ASVs. I guess at this point I need to perform the analysis directly in Dada2.
Thanks again

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4

This will give you more control!

Let us know if you have any other questions.

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