extract pathogens from metaphlan3 results

Question

[serene.s]

Hi Guys! I am trying to analyze my metagenome data using the MetaPhlAn3 tool, I created a spreadsheet of all the species that were present in each sample. Now my goal is to find out the pathogens from that list. So, is there any tool that can do it for me or any database which can take the list of the species that I have? Or do I have to run a whole pipeline again for that matter? Guys, please suggest options as I am new to metagenome analysis.

Thanks in Advance Saraswati

[cpad0112]

Metaphlan3 uses chocophlan database which is proprietary. Hence you would not know the presence of pathogens unless Huttehower labs provides another tool to extract organisms by category. There are two ways to do what you want:

1. Restart the analysis, but instead of using metaphlan3, use pathogen databases such as microphenodb, mypathogendb etc.
2. I guess you can get 7 level classification from metaphlan3. Extract the genus and species level information (identified) for each organism and search the pathogen database with this information.

[serene.s]

Hey @cpad0112 Thanks for responding, I have already extracted the species from the MetaPhlan3 results but now the problem is that I am not able to find out any tools or databases that can directly take that list as an input for detecting the pathogens from that. I guess I have no other way than to find a whole pipeline for pathogen detection.

Thanks Saraswati