How to start analysis with ASV data?

Hello Qiime2 community,
I have a doubt about how to start the analysis of ASV data. In our lab, we would like to do microbiome analysis at the species level. However, we are having problems because one species has occurred more than once. How can we proceed with species richness analysis, alpha diversity, and univariate analysis? Should we merge the ASVs or is it okay to proceed with more than one species?

Thank You

Hi @Rishikesh12,
This is not abnormal in my opinion. Each ASV are unique sequence but more than 1 unique sequences can be assigned to a species.

I would keep your asv separate for species richness analysis, alpha diversity, and univariate analysis steps. If you are interested in running ancom-bc, I would collapse to the species level for that analysis step if you are interested in the species level analysis.

Hope that helps :turtle:

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Actually I pulled out data from qiime to start analysis in R. ASV separate for all analysis, actually I didn't understand asv separate for species richnees and alpha diversity analysis? Is it possible to do analysis in qiime2 at species level ? Can you share me a any research paper where all analysis was done using ASV data ?

Thank you

Hi @Rishikesh12,

I was assuming that you were using qiime2 but I assumed when you were talking about species level analysis, you were running qiime taxa collapse at the species level and then running species richnees and alpha diversity analysis. I would recommend not grouping your asv into taxonomically labelled species before running diversity analysis.

It is possible to do species level analysis by running qiime taxa collapse.

There is a lot of papers that run asv analysis.
Here is one:

Also here is the link to all the papers that cite dada2 - I would say that most of these papers have all their diversity analysis at the asv level.,3&hl=en
Hope this helps! :turtle:

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Thank You for information.
Can you please tell me the plugin or command for qiime taxa collapse for species level analysis?
I used phylogenetic tree for diversity calculation so for species level analysis can i use same or is there any different way?

Hi @Rishikesh12,
Unfortunately there is now way to build a phylogenetic tree in qiime2 with a feature-table collasped to the species level. If you want to do diversity analysis at the species level, you will need to run core-metrics and skip core-metrics-phylogenetic.

Here is additional information that another moderator gave when a user asked a similar question but regarding genus level analysis.

Hope that helps!

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