MetaPhlAn - help with customising database

Microbial community profiling MetaPhlAn
1

Pasted from here: https://github.com/biobakery/MetaPhlAn/issues/209

Hi!

First, thank you for providing MetaPhlAn! I’m excited to use it.

I would like to use a specific genome catalogue, namely OceanDNA, Nishimura & Yoshizawa, 2022, as part of my reference database.

I could find the Customizing the database section in the docs, however it’s unclear to me how to generate the SGBs and identify the markers for that MAG catalogue. Is there a workflow/tool/script to do that?

Or alternatively, would you consider adding OceanDNA to your next database update?

Thank you for any assistance you can provide!

V

2

Hi @vinisalazar
Unfortunatelly, there are not scripts available to generate new MetaPhlAn databases and we did not add yet this specific genome catalog to our genomic database. However, it looks as an excelent addition and we will include it in the next MetaPhlAn release.