June saw the annual meeting of Galaxy developers and users at the Galaxy Community Conference 2024 in Brno, Czechia. This year over 150 participants came together to share updates to the Galaxy platform and present use-cases showing how Galaxy has enabled high-quality science through providing computational infrastructure and software support. Galaxy has established open computational servers in the United States, Europe and Australia alongside a suite of tools to give scientists the opportunity to process and analyse data of any size without the need to establish or use a local High Performance Computing service.
During the 4-day conference ERGA, the Vertebrate Genomes Project and the wider Earth BioGenome Project were well-represented, demonstrating how Galaxy fits into a distributed model of reference genome generation. Updates to the VGP pipeline were presented by Delphine Lariviere and Linelle Abueg, showcasing how they have used a Galaxy server at the Vertebrate Genomes Lab to assemble over 150 species. They also introduced the efforts made to assist manual curation of the assemblies. The VGP uses their published pipelines and training material to give instructional workshops on how anyone can use Galaxy to assemble a genome without access to an HPC or even needing to install any software.
Within the ERGA framework, Tom Brown presented how collaborators from Galaxy EU are helping ERGA to establish a review system for genome assembly via the ERGA Assembly Report (EAR) and assist the genome annotation community in installing necessary tools and developing workflows that enable researchers to annotate their favourite genome using best-practice tools and pipelines.
You can learn more about the VGP’s efforts to assemble vertebrate genomes in their paper published in Nature Biotechnology and read about ERGA’s efforts to benchmark annotation tools and workflows on a diverse range of organisms in their report from last year’s BioHackathon Europe.
The Galaxy Community Conference 2024 presented a fantastic opportunity for developers, systems administrators and researchers from the genomics, astronomy and material science communities to come together and hear about the latest advancements in Galaxy and its uses. Many thanks to the organisers and especially Björn Grüning and Anton Nekrutenko for their support given to the biodiversity genomics community.
About the Author
Tom Brown is the coordinator of the ERGA IT & Infrastructure Committee and also participates in the ERGA Sequencing & Assembly and Annotation Committees.
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