Question

When assembling a genome what does the N50 score measure? Do we normally try to maximise or minimise the N50 score?

Answer 1

N50 score is the median contig size of the genomic assembly. It is further defined as the minimum contig length needed to cover 50% of the genome. It's used to evaluate the quality of the assembly of genomes. Yes, we often try to maximize the N50 score because "the higher, the better" but, there's no reason to minimise the score intentionally. We can increase the N50 by eliminating sequences which are bound to cause proteins like, short repetitive stretches etc.