functional analysis

General Discussion
1

Sorry for bombarding you with my questions.
Apart from PICRUSt2 ( PICRUSt2: An improved and extensible approach for metagenome inference | bioRxiv
) , what other tools can we use to predict functional analysis of amplicon sequencing on ITS?

2

If you read through the published version of the PICRUSt 2 paper, you'll see that they compare against other tools. Some of these tools only require taxonomy, thus not requiring any specific marker gene information.

Here are some other tools that come to mind:

There are likely many more tools out there, I'm sure the community will recommend a variety of other tools too. :slight_smile:

-Cheers!

3

thank you very much
I thought that FunGuild doesn't go into deep in other terms it only tells you if it's Saprotrophic fungi ,Ectomycorrhizal fungi , Arbuscular mycorrhizal fungi , Wood decomposer fungi , Plant pathogenic fungi.
in you opinion what's the best one among FunFun , picrust2 and FunGuild

4

That is why I said:

I honestly could not say. In fact, some tools might work better for certain data sets / environment types over others. Many users will try several tools and decide which makes the most sense given their study system.

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5

@SoilRotifer
Happy new year
Can you please provide clarification regarding the disparities in function analysis prediction capabilities between picrust2 and funfun? Despite my attempt to comprehend through the documentation, the distinction between the two tools remains unclear to me.

6

I've not used FunFun before. The only thing I can recommend is to keep reading / re-reading the associated papers, and actually play with the tools on your data. Perhaps someone else with more current experience using these tools and can comment here?

-Good luck!

7

Thank you, sir.
May I publish this question as a new issue?

8

I do not think it'll be necessary. If others have ideas or thoughts on this they'll respond to this thread.

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