Database differences in MetaPhlAn

Microbial community profiling MetaPhlAn
1

Hi everyone,

I’m starting to go deepen in metagenomics bioinformatic analysis. Previous to post my question I google it my doubt without success.

From the next webpage, it could be possible to download the last release of MetaPhlan databases:
http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.

Nevertheless, which are the differences between mpa_v20_m200 database vs mpa_v29_CHOCOPhlAn_201901 v293 CHOCOPhlAn…

And also, in my pc I have metaPhlan2 with ancient mpa_v20_m200. How can I update the database? One option will be the steps described by Francesco in the next link: https://forum.biobakery.org/t/run-metaphlan-offline/2349

Thanks on advance,

David.

2

Hi @D11
Thanks for getting in touch. The v29, v293, etc were transitional versions between version 2 and version 3. I would recommend you to move directly to v30. You can find the main updates in our last manuscript: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife
For updating to the last version of the database, you should also update the version of the code. I recommend you to install it via conda. You can find the installation instructions in the following link: MetaPhlAn 3.0 · biobakery/MetaPhlAn Wiki · GitHub