[jakobnissen]

Indeed you are right, that would be much easier. DNA assembly is an insanely hard computational problem. The issue there is that it's difficult to actually build a sequencing machine that can sequence more than a few hundred base pairs before it stops.

Why that is hard depends on the approach the machine takes to sequencing. With the "sequence by synthesis" approach, the problem is that you need one or two chemical reactions per base, and any yield much lower than 100% will quickly degrade the product after a few hundred cycles.

Nanopore uses a different approach and can indeed produce very long reads, with the tail of the distribution being tens of thousands of base pairs. Not sure what the bottleneck for the length is there.