functional analysis

[Dali (med ali)]

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?

[SoilRotifer (Mike Robeson)]

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:

• FunFun: ITS-based functional annotator of fungal communities. I've not used this tool, but looks worth investigating.
• FunGuild. This provides a higher level of annotating the functional guild of fungi.

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

-Cheers!

[Dali (med ali)]

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

[SoilRotifer (Mike Robeson)]

@Dali

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.

That is why I said:

@SoilRotifer

This provides a higher level of annotating the functional guild of fungi.

@Dali

in you opinion what's the best one among FunFun , picrust2 and FunGuild

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.