Non-Microbial profiling

Good morning,
I’m new in bioinformatics.
I’ve read the metaphlan3.0 manual and it says that analysis with metaphlan allows to reach the spice-level resolution for bacteria, archeae, viruses and eukaryotes but my outputs show only bacteria abundance, am I doing something wrong?

The command I use is :

metaphlan file_name.fastq --input_type fastq > output_file_name.txt

Which eukaryotes are included in the database?
Is there any possibility to consult the metaphlan database?
Is it possible to incorporate another database to my analysis?

Thank you for your help.

A list of species included in the database is available in the marker info file here
You cannot incorporated another database to MetaPhlAn, but you can expand it with the new markers for the species of interest.

1 Like

Hello Francesco,

Some markers not present in this file are present in the fasta file (mpa_v30_CHOCOPhlAn_201901.fna), can the species they belong to be found by metaphlan3? If yes, under what taxonomy would they appear in the profile tsv file?

Thank you very much for your help,