The plummeting costs for sequencing over the last decades, allow whole genome resources to be built in a single lab, for a single project. While accessible to most, the process still demands informed decision-making and navigation through potential pitfalls.

High-quality genome assemblies are key for deciphering the biology of an organism, paving the way for diverse downstream analyses:

genetic variations: Identify mutations linked to disease, adaptation, or other phenotypes.
gene function: Delve into the roles and networks of genes within the organism.
evolutionary history: Chart the path of genetic divergence and understand relationships between species.
comparative insights: Analyze similarities and differences across genomes to uncover broader biological principles.

Genome assembly has been revolutionized by long-read sequencing technologies, particularly by PacBio HiFi and Oxford Nanopore Technology. These technologies overcome the limitations of short-read methods, in assembling complex genomes with high levels of repetitive regions. As a result, they are currently the obvious choice for generating de novo reference genomes.

While a number of assembly pipelines and algorithms exist, informed decision-making, from defining your project goals and crafting optimal sequencing strategies to assessing the final assembly, each step holds critical implications for success.

Ultimately, the reward is a reference genome of your target organism that will lay the foundation on which downstream experiments can be built.