Genomics in focus: Galaxy features at the 31st Plant & Animal Genome Conference
The international Galaxy Project recently participated in the 31st annual Plant & Animal Genome Conference (PAG31), the largest ag-genomics meeting in the world. The team hosted a hands-on workshop and offered presentations on next-generation sequencing data analysis, training, and the Vertebrate Genomes Project. Galaxy's dedication to open-source, FAIR data access, and comprehensive analyses shone through at PAG31.
Galaxy workshops leveraged the platform’s tools, workflows, and existing training materials. Workshop attendees experienced running their own microbiome analyses on reference data, and the assembly and annotation of microbial genomes. One workshop emphasised the integration of long and short-read sequencing methods and highlighted the significance of predicting protein structures using ColabFold, bridging genomic sequencing data with functional proteomics analysis. Participants agreed they had gained a deeper understanding of Galaxy's capabilities.
A spotlight on the Galaxy Training Network (GTN) emphasised its collaborative, open, and FAIR approach to scientific training materials. With over 300 tutorials authored and reviewed by a global community, the GTN serves researchers, educators, and scientific tool developers.
The Vertebrate Genomes Project (VGP) took the spotlight at PAG31, offering a series of talks that delved into the project's ambitious goal of generating phased, error-free, chromosome-level, near-complete, and annotated reference genome assemblies for all ~75,000 extant vertebrate species. Galaxy is a linchpin in the VGP's mission, facilitating seamless data integration, analysis, and collaboration among researchers. Galaxy is helping to overcome challenges related to genome-wide alignments, phylogenetic tree inference, universal gene nomenclature, and comparative genomics of specialised traits within the VGP's Phase 1 scientific studies, in which a representative species from (nearly) every vertebrate order will be assembled and released. Extensive documentation to guide users implementing the genome assembly workflows has been prepared by Dr Anna Syme, BioCommons bioinformatician and Galaxy Australia workflows specialist.
The recent paper ‘Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy’ identified how Galaxy is a crucial component in the VGP methodology and underscores Galaxy's pivotal role in enabling cutting-edge genomic studies on a global scale.
The ‘Justice, equity, diversity and inclusion’ workshop investigated how to acknowledge and address systemic injustices in genomics, and encourage and establish an environment where the field can realise its full scientific potential while embracing social responsibility and inclusivity. Prof Carolyn Hogg’s presentation, ‘Implementation: Genomic Resources’, highlighted the role Galaxy Australia plays in her work and emphasised the importance of integrating tools like Galaxy in the pursuit of justice, equity, diversity, and inclusion within genomics. Carolyn is co-lead of the Australasian Wildlife Genomics Group at the University of Sydney, Science Lead and Chair of the Bioplatforms Australia Threatened Species Initiative, and we are thrilled to see her regularly championing the use of the Galaxy Australia service by her genomics and genetics research peers.
This story was adapted from the detailed meeting report on the Galaxy Community Hub, where you can learn more about Galaxy’s involvement in PAG31.