Constructing custom database de novo

Microbial community profiling MetaPhlAn
1

Hi Guys,

I’m currently working on human gut metagenomic data and want to make custom MetaPhlAn and HUMAnN databases based on public data such as Unified Human Gastrointestinal Genome (UHGG).

I have noticed the docs on GitHub and many valuable discussions such as customizing-chochophlan-panproteome-and-metaphlan-marker-gene-databases-with-new-taxa/2814 and github-issue-103, but most of them began with the existed databases. I was wondering whether there is any tutorial or suggestion for creating custom databases de novo.

Besides, it’s hard to keep these databases “up-to-date” with the rapid increase of bacterial genomes, and some researchers may be interested in a specific region (such as the human/mouse gut). Thus, tools for MetaPhlAn and HUMAnN to de novo construct databases would be very useful and necessary.

Best regards,
Ming

2

Hi @songmingl
Unfortunately, there is not a code or a tutorial available to generate a custom metaphlan database. But the method is well described in the last manuscript in case you can give it a chance to implement it: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife

3

Thanks for your reply! I will try this later.