StrainPhlAn for detection of known strains in mixed-strain samples

Microbial community profiling StrainPhlAn
1

Hi,

I have nanopore metagenomic samples and I am looking to detect the presence of 4 known L. monocytogenes strains (reference genomes available).

I have seen it suggested to:

  • Use a single reference genome for mapping
  • Then rely on StrainPhlAn’s marker gene knowledge to differentiate between the strains

My understanding however is that StrainPhlAn reconstructs a single consensus sequence per species per sample from marker genes, meaning:

  1. If a sample contains multiple strains simultaneously, the output would be a chimeric consensus rather than detection of individual strains — is this correct?

  2. Is StrainPhlAn designed for reference-based detection of specific known strains, or primarily for phylogenetic comparison of the
    dominant strain across samples?

Thanks!