Regarding phasing variants

[mdrishti]

Hi @chrisquince ,

I am trying to phase different variants and find out if a pool of E coli genomes (derived from the same strain, but evolved and therefore exhibit many gene variants) show different sublines of the same E coli strain, more like the quasi species concept from viral populations. I read the research article about DESMAN, but I am not completely sure if this is what I need. On one hand, I see that there are examples to resolve the strain diversity for E coli in the paper, but on the other hand, I am not sure if these strain level differences include divergence
at SNP/MNP/Indels (all for the same strain)? Any insights will be super useful.