The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

The quality of genome assemblies has improved rapidly in recent years due to continual advances sequencing technology, assembly approaches, and control. In the field molecular ecology, this led development exceptional that will be important long-term resources for broader studies into ecological, conservation, evolutionary, population genomics naturally occurring species. Moreover, extent which a single reference represents diversity within species varies: pan-genomes become increasingly ecological resources, particularly systems found have considerable presence-absence variation their functional content. Here, we highlight technology raised bar provide guidance on standards achieve genomes. Key recommendations include following: (a) Genome should long-read except rare cases where it is effectively impossible acquire adequately preserved samples needed high weight DNA standards. (b) At least one scaffolding approach included with such as Hi-C or optical mapping. (c) carefully evaluated, may involve utilising short read data polishing, error correction, k-mer analyses, estimating percent reads map back an assembly. Finally, most valuable if all methods are made publicly available utility further verified through examples. While these based current anticipate future push ecology community continue adopt new approaches attain highest assemblies.