Indicator species analyses

[Antani (Edoardo Scali)]

Is there any QIIME2 plugin for running Indicator species analyses after ASVs classification?

Thank you for your help.

[crusher083 (Valentyn Bezshapkin)]

Hello,

Honestly, I am not sure what is meant by "indicator species", but it sounds very similar to what q2-sourcetracker and q2-feast do, find more information in the linked thread.

sourcetracker2 plugin?

Hi there! I was trying to use sourcetracker2 with my QIIME2 feature table. I’m having some issues with the biom file I exported from qiime in the sourcetracker2 package from github, and I see some evidence that there is (was?) a q2-sourcetracker plugin. I thought I’d try and see if I could utilize the qiime plug in if it exists, to make the process simpler… however it looks like the q2 package is gone? Or I’m just looking in the wrong places! Anyway, I’m just wondering if a q2-sourcetracker2 p…

Hope that helps,
Valentyn

[Antani (Edoardo Scali)]

Hy @crusher083,
thank you for your help.

By searching online, I find that sourcetracker is used assissing the presence of contaminants in samples. Is that correct?

Anyway, what I would like to do is to analyses those species (Indicator species) that are used as ecological indicators of community or habitat types, environmental conditions, or environmental changes.
Here is a resource about indicator species analyses: Indicator Species Analysis: A Useful Tool for Plant Disease Studies - PubMed

Do you know if there is a plug in for this?
Thank you so much!

[crusher083 (Valentyn Bezshapkin)]

Hello,

Please take a look a sourcetraker tutorial. It uses Bayesian methods to estimate hypothetical bacterial abundance with respect to metadata. (finding a distribution of bacteria in certain environments, such as sewage, initially)

If you want to replicate analysis from the article, you need to do it outside QIIME, as there are ko such plugins. If you think it's a useful analysis method feel free to contribute with a plugin

Cheers
Valentyn