Can metaphlan calculate alpha diversity and beta diversity

[yunli...@gmail.com]

Hi all,
Can metaphlan calculate alpha diversity and beta diversity?

Thanks,
Yun

[Duy Tin Truong]

Hi Yun,

Currently, Metaphlan does not have that feature.

Cheers,
Tin

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[Ming Liao]

Hi, Yun

I think the current metaphlan2 is able to output the biome file, which can be applied to QIIME and make some diversity analysis (http://qiime.org/scripts/core_diversity_analyses.html).

https://bitbucket.org/biobakery/metaphlan2
Output arguments:
--biom biom_output, --biom_output_file biom_output
If requesting biom file output: The name of the output file in biom format

[Robert Kwapich]

Alpha diversity for 16S is concerned with (not looking at all metrics - only "observed OTUs") with number of "unique" OTUs for each sample. I guess you have to be careful as you would first need to stratify your output.

Have a look at this recent paper: https://www.nature.com/articles/s41522-017-0022-5.pdf
(methods section).

They are stratifying output to SPECIES level - there are reasons for that, as 16S OTUs respond "roughly" (although not quite excactly) to species.

I.e. in this sense "alpha diversity" would be number of identified unique species with. It turns out that they've rarefied the dataset manually, so you'd have to run metaphlan several times on your rarefied dataset to obtain that. IMHO rarefaction is good, as unequal number of reads may produce spurious correlations - especially if you work on relative abundances.