The other big complexity is the self-similarity of the genome. To sequence, the genome is duplicated, then sharded physically into many overlapping tiles around an average length, each tile starting at a different position. Each sequence is determined in parallel, and then the shards have to be reassembled computationally (really, this is a post-sequencing process, but is critical to being able to call the result a "sequence" rather than a bag of reads).

If the genome in question contains a lot of regions that are similar to each other, the algorithms that do the assembly will get confused.