Calculating Alpha and Beta Diversity with Metaphlan3 Rel Abund

Good morning!

Thank you in advance for your help! I am pretty new to this analysis. I have run my samples through metaphlan3 for a microbiome analysis and am quite happy with the output relative abundance tables. How do I move forward to calculate my alpha and beta diversity? Can this be done in metaphlan3?

I am also trying to normalize my data so I can normalize resistance genes. Is there a way I can observe what the average length of alignment was to the database? And, would I be able to observe the number of alignments to the bacteria sequence per sample?

Thank you so much!


Hi @jlhaller
Thanks for getting in touch. You can find a tutorial of how to perform alpha and beta diversity analysis from the metaphlan data in this link: Metagenomic Visualizations · biobakery/biobakery Wiki · GitHub
Regarding your second question, the abundances of MetaPhlAn, are already normalized by the total coverage of the microbial species. This is why you see the abundances in the form of relative abundance. If you are interested in the specific of the alignment against the MetaPhlAn database, I would suggest you to investigate the output SAM file from Bowtie2. You can save this files after the MetaPhlAn execution using the parameter -s