Hi all,
panphlan claims to be able to track unkown strains but how is that possible? Because you allways have to supply a database like Ecoli. What if you do not know what bacteria species are in the sample?
Cheers
PanPhlAn and StrainPhlAn are approaches for identifying novel strain-level diversity within known species. They are designed in tandem with MetaPhlAn such that you can identify species in your community first with MetaPhlAn and then (if the species have sufficient read depth) investigate them at the strain level afterward with PanPhlAn or StrainPhlAn.