High resolution analysis reference genome download

Microbial community profiling PhyloPhlAn
1

Hi @franzosa
I want to know in the high-resolution analysis of a known species the reference genomes are selected on what basis. In the example tutorial, they are downloading 200 E.coli genomes from GenBank but I want to know if are there any parameters on the basis of which those 200 genomes are selected or randomly.

Thanks

2

Hi, you can assume that the 200 E. coli genomes are randomly selected and are only used to provide more phylogenetic context for the user’s MAGs that are assigned to the same species/SGBs.

Thanks,
Francesco