Community-driven standards development for reference genome generation
Creators: name: Brown, Tom
name: De Panis, Diego
name: Libouban, Romane
name: Momin, Saim
name: Kadkhodaei, Arash
name: Bretaudeau, Anthony
name: Grüning, Björn
name: Mazzoni, Camila
Publisher: name: F1000 Research Limited
Year: 2024

description: In the face of current threats to biodiversity globally, a number of initiatives and consortia are coming together to provide genomic resources to help us understand mechanisms and drivers leading to loss of species and ecosystems. Among these initiatives, the European Reference Genome Atlas (ERGA) aims to bring together researchers across the European continent, creating standards and protocols to allow the distribution of tasks from identifying and sampling key species of interest, extracting and sequencing genomic material, processing and generating high-quality genomic resources and ultimately providing these resources to the public in the form of genomic data and high-quality reference genomes.<br>
To generate high-quality reference genomes and annotate the functional elements of those genomes in a democratised and distributed manner, we must provide tools, workflows and evaluation procedures to the community. ERGA has already made strides to bring together and standardise protocols and workflows among the community, but there remain areas which require improvement and expansion. In particular, many workflows and tools have only been robustly tested and benchmarked against a small fraction of organisms, mainly focused on vertebrates, lepidoptera, or model organisms. Complementary to the work achieved by the ELIXIR, Galaxy (Galaxy Genome Annotation, EuroScienceGateway) and EBP (VGP, ATLASea) communities, researchers from ERGA are installing tools and developing workflows for Galaxy to assemble and annotate genomes from any taxonomic group and with any input dataset to the high standards set by the Earth Biogenome Project (EBP).<br>
A fundamental concept of ERGA’s model of distributed genome generation is on establishing and enforcing standards of research outputs, rather than dictating single tools and workflows that should be followed in every case. As the diversity of organisms and data types increases with the number of species sequenced, we anticipate an increasing number of “best-practices'' dedicated to individual cases. As such, we have developed a framework to assist the community review of reference genomes after the generation of a standardised ERGA Assembly Report (EAR) and have begun benchmarking software across the Tree of Life.<br>
This talk will demonstrate how we have brought together multiple research communities to develop tools and workflows to generate and evaluate genome assemblies and annotations in Galaxy. ERGA and the EC-funded BGE project are publishing our workflows openly for all to use on WorkflowHub and encouraging researchers to test their deployment inside the GalaxyEU framework (https://workflowhub.eu/programmes/33). We will report on our results and efforts at the BioHackathon 2023 (Brown et al. https://doi.org/10.37044/osf.io/fy49g) in the evaluation of genome annotation tools across the Tree of Life for determining the best automatic genome annotation for certain clades. Furthermore, we will present how researchers can use the developed Galaxy workflows to produce evaluation reports, which can be reviewed by the genomics community and used to maintain the high standards expected of the resources published by ERGA and the EBP.