Thanks for the comment. My intention of this article was to introduce the assembly process and presenting the bigger picture. Alignment of reads would not be feasible without a reference or at least a closely related strain, me and my colleagues believe with better quality reads assemblies would give more information about the genomes especially the mammalian ones including Human. My current research heavily uses assembly graph from assembly process which is otherwise discarded. So I was interested in linking my assembly article to coronavirus given it’s a simple experiment for an article to read and the data is publicly available as well.

I really appreciate if you’d share how you’d decide on the reference set of sequences for the real-time mapping scenario. It seems interesting as I’m working on binning and have challenges whenever a reference of a closely related reference is not available. As of now we rely on assembly graph and oligonucleotide composition information.

Thanks