[robwwilliams]

What you are getting at is now called a “pangenome assembly”. Several high profile papers earlier this year, one by Guarracino and Garrison in Nature.

A pangenome is a complex graph model that weaves together hundreds or more genomes/haplotypes—usually of one species, but the idea can extend across species too, or even cells within one individual (think cancer pangenomes).

On the idealized human pangenome graph each human is represented by two threads along each autosome, plus threads through Chr X, Y, and the mitochondrial genome.