[BbzzbB]

Maybe someone can correct the details since it's been a few years I done this, but we sequence DNA by PCR. Roughly, (1) breaking it up in small pieces and split strands, (2) mixing it with an enzyme that completes each single strand, (3) repeat 1 and 2 a bunch to multiply the strands many times over to make the solution a sense DNA juice, (4) pass it through a machine that'll sequence thousands of these small strands and (5) align these short DNA sequences with a software that matches unique sequences.

I did it with COI gene, which is just a short (1000ish base pairs with our snails IIRC) sequence of purely random ATGC base pairs. Lots of unique sequences make the short strands easy to match, just get a bunch of 10-15 BP bits and you can match the whole thing.

Now if your gene is 62M BP of repeating palindrome sequences, you can imagine how hard it would be to align random pieces sequenced as it will be very hard to find unique sequences to match.

[inciampati]

We don't use PCR anymore! It's direct sequencing of the primary DNA. We can read single molecules. That's the quiet revolution in nanotechnology that's driving all these complete assemblies.