My aim is to identify well-known strains in my own samples. For example, in a recent journal article titled RNA Landscape of the Emerging Cancer-associated Microbe Fusobacterium nucleatum, the introduction contains
… we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains— F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii, as well as F. periodonticum
Can StrainPhlAn do that? I can’t find anything in its user guide that suggests I could identify Fusobacterium nucleatum subsp. nucleatum, for instance. Is StrainPhlAn only for calculating the number of SNPs to a species reference genome?
Step 2. Obtain the sam files from these samples by mapping them against MetaPhlAn database
Step 4. Extract the markers of Bacteroides_caccae from MetaPhlAn database
Isn’t the database called ChocoPhlAn? MetaPhlAn is the name of a software.