Diversity analysis after metaphlan2

Question

[biobiu]

Hi, I've ran metaphlan2 on shotgun metagenomics sequencing data and want to perform diversity (alpha and beta) analysis.

Is there some tools allows calculating alpha diversity metric to each sample (like shannon), and beta-diversity metrics bewteen pairs of samples (like jaccard or bray curtis).

I undestand that some metrices requires moving to absolute counts but I know that metphlan1 had this option.

Thanks!

Answer 1

[DriesB]

According to MetaPhlAn2's Bitbucket, you can export as BIOM. I would expect you to be able to import that into the phyloseq package, but have not tested this yet.

[DriesB]

I'm also in the process of analyzing shotgun sequencing metagenomics data. Please give some input to my question here, if you have recommendations!

[dpc]

Hi.... did you analysed your shotgun data? I need help. I am doing analysis with metaphlan.

Answer 2

[evoBio]

With vegan package you can calculate different diversity metrics and perform ordination analysis as well. If you want to perform statistical analysis I would recommend metagenomeSeq.