Hi Biobakery team,
I read the StrainPhlAn paper quite a few times, but I still have couple of lingering questions about the StrainPhlAn3 that I hope to check with the team themselves. So I apologize in advance for these 2 simpleton questions.
Would it be correct to understand that StrainPhlAn outputs MSA consisting of strain-specific consensus sequence. And each strain-specific consensus sequence represents the most dominant strain of a bacterial of interests from a sample. Therefore, given enough reads for a bacteria of interest in a sample, then StrainPhlAn can output 1 strain (most dominant) from that 1 sample.
Is it also correct to understand that the generation of the strain-specific consensus sequence is essentially the concatenation the dominant markers found in a sample that satisfy the marker threshold (default: at least present in 80% of the samples with bacteria of interest)?