Typical Assembled Genomes

Genome assembly is different from other scientific tasks, because it is closer to engineering than science. In case of assembly, the final answer is precisely definable and the goal is to get as close to that answer as possible. Like in all other engineering problems, three factors - quality, time and cost - need to be balanced to find an optimal solution. With large amount of money, it is technically possible to derive the correct answer very precisely. That is different from scientific questions such as Fermat’s last theorem, where intellect is often the bigger obstacle. The interplay between money, an engineering attitude and science places genome assembly into a separate class from other sciences. Due to this engineering aspect, assembly programs rarely obtain full chromosomes of complex genomes in the end. Instead, the assembly process results in many smaller blocks (called scaffolds and superscaffolds). Closer they are in size to the fully assembled chromosomes, the better.

N50 is a simple measure to compare the sizes of various versions of the assembly. It constitutes of