Accessing genome assemblies
In the early days of genome sequencing, short reads were primarily used to assemble genomes, leading to short, fractured assemblies. Scientists would go to conferences and talk about how they had gotten the assembly for their favorite organism down to 10,000 contigs instead of 50,000! This meant it was often unclear which chromosomes these contigs belonged to, or what order they went in. Scientists would try to scaffold the contigs by looking for markers to place them in general areas on chromosomes, and they would engage in painstaking efforts to close the gaps. But if you have a human genome of 3 Gb and 24 chromosomes, you would imagine that you might like to get 24 contigs if you could! (Or, better yet, 48 contigs in total by resolving the haplotypes of the diploid genome.)With the advent of long-read sequencing, this has changed dramatically. We are now able to routinely assemble entire microbial chromosomes with ease (often called “closed genomes...
