Production of reference genomes of EBP-quality at scale requires a high level of automation and quality control. We aim to continue updating the de novo genome assembly pipeline in production at the CNAG. Plans include the addition of Hifiasm for assembly of PacBio HiFi data, testing and incorporation of Hi-C mapping and scaffolding modules, automated decontamination, as well as mitogenome and chloroplast assembly (developed but requiring further testing).

An additional standardized assembly evaluation and genome report module will be added when its development is finalized by the BGE Assembly Development task and the ERGA Sequencing and Assembly Committee.

This project is funded by the Institute of Catalan Studies.


All work will be carried out by the CNAG Genome Assembly and Annotation Team.


Tyler Alioto (PhD, the Genome Assembly and Annotation Team Leader at CNAG) will coordinate the project.