how

[timeresistance1996]

How does Pavian define the pathogen. Is it based on species classification names using software such as Kraken？

[gregorysprenger]

Yes. I would recommend you read through the pavian paper.

[fbreitwieser]

Thanks for responding @gregorysprenger . What's a pathogen or not the tool cannot define, it can just show you what species are present, and those species which are more present in some (pathogenic) samples and not in others may be pathogens.