Is there a way to use files from Nanopore in Qiime2 ?

General Discussion
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Hello! I want to use files from Nanopore machine in Qiime2. I have looked through some questions and answers, but they have been quite a while. Hence, I want to ask similar topic at the moment.
--------------My all preparations are as below--------

  • What specific kit chemistry (what version of what kit)? : NEBNext Ultra II End Repair/dATailing Module, NEBNext Quick Ligation Module, NEBNext Blunt/TA Ligase Master Mix, NEBNext FFPE DNA Repair Mix
    MinION Mk1B Starter Pack
    Native Barcoding Kit 24 V14

  • What flowcell type (v.9.4.1? the new 10.3?)?
    Flow Cell (R10.4.1)

  • Are you using the latest basecalling with Guppy? What version? Or are you using Bonito instead?

I am trying to use Guppy.

With the information above, Is there anyway to conduct analysis in Qiime2 ?
(Hoping some possible ways,
*Chat GPT told me that using Guppy for basecalling, and use Porechop in Q filtering.

Would you recommend the processes or software tools to fully use Qiime2 with the Nanopore output file ?

Many thanks in advance.

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Hello @SingeunOh,

Thanks for proving all the technical details. That specificity is very helpful.

Call you tell me more about the biological specifics? What microbe(s) did you sequence? What gene did you amplify or did you target the whole (meta)genome or (meta)transcriptome?

What's the biological question you are trying to answer? :male_detective:
(Or, what claim are you gathering evidence in favor of to argue that it is true?) :judge:

Cool :sunglasses:
Remember, language models are parroting past text. They don't inherently have a source of truth. :parrot:

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Thank you colin for your detailed responses. We will try to amplify the whole microbiota from the feces of animals.(with the region of 16S rRNA V3-V4 region first, but more region of 16S rRNA later) Hence, we will use it for metabarcoding of microbes within the feces.

The first biological question is which species of microbes are in,
and the second question is whether the difference of alpha(beta) diversity of the species exist accroding to some factors (sex, infection status, or etc.).

If more information is needed, then please reply once again.

Thank you for your helps !!

4

Thank you for telling me more!

Qiime is a great fit for V3-V4 reads, stool microbiomes, and alpha&beta diversity! Let's see how we can best work with Nanopore data.

Have you discovered MetONTIIME? It's a nanopore pipeline for Qiime2 that sounds like a great fit for your data set.

Let us know what you try next.

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Thank you colin! I appreciate all the help you provided. I will try the method that you mentioned. If more questions arise, I will reply them once more. Have a great day !

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