The bioBakery help forum

Input for Panphlan

Dear Developers,

Can we use Humann3 output or Metaphlan3 output as input for Panphlan3?
Because I don’t have the access to fastq file of the metagenomic sequences.



Unfortunately this is not possible. Definitely not with MetaPhlAn results which focuses on markers gene while PanPhlAn needs the full pangenome of the species.
As for HUMAnN, it uses only the representative sequences of UniRef90 clusters while PanPhlAn uses all genes across multiple reference genomes and then aggregates the information they convey into UniRef90 families. Thus, there might be some strong bias in the results.

Hope you will manage to get access to the fastq as it might be the easiest solution.


Hi Léonard,

Thank you so much for your response.
You explained this very clear.
I will try to get access to the fastq as you suggested.