How to calculate alpha beta diversity

Microbial community profiling MetaPhlAn
1

Hi @fbeghini
Is it possible to calculate the alpha-beta diversity analyses using the metaphlan3 pipeline? If yes how I can I do so?

Thanks
Saraswati

2

Hi Saraswati,
No, MetaPhlAn does not include a script for alpha diversity calculation. Iā€™d suggest you to check some R packages like vegan or phyloseq.

3

On a related note, how can you use MetaPhlAn data to calculate alpha diversity since it is marker based not read based?

Thanks,

Sarah

1 Like
4

Thanks @Sarah_Highlander for putting it very straightforward.

5

You can treat species like OTUs. alpha.div from rbiom (https://cmmr.github.io/rbiom/reference/alpha.div.html) can take a species x sample dataframe and estimate several indexes.

į§

6

Thank you! How would you recommend to rarefy a typical mpa output table with relab using this tool? And which diversity measures do you recommend?
Chers,
Stef

1 Like
7

@fbeghini which diversity measures do you recommend for relative abundances from rbiom? And how do you deal with varying sequencing depth?
All the best,
Stef