Automated reference genome assembly in Galaxy – An update
Creators: name: Linelle Abueg
name: Larivière, Delphine
name: Nadolina Brajuka
name: Gallardo, Cristóbal
name: Flores, Marc Palmada
name: Ostrovsky, Alex
name: Ko, Byung June
name: Grüning, Björn
name: Arang Rhie
name: Nekrutenko, Anton
name: Pickett, Brandon D.
name: Rabbani, Keon
name: Antunes, Agostinho
name: Balacco, Jennifer R.
name: Chaisson, Mark
name: Haoyu Cheng
name: Collins, Joanna
name: Couture, Melanie
name: Denisova, Alexandra
name: Fedrigo, Olivier
name: Gallo, Guido Roberto
name: Giani, Alice Maria
name: Grenville MacDonald Gooder
name: Horan, Kathleen
name: Nivesh Jain
name: Johnson, Cassidy
name: Heebal Kim
name: Lee, Chul
name: Marques-Bonet, Tomas
name: O'Toole, Brian
name: Secomandi, Simona
name: Sozzoni, Marcella
name: Tilley, Tatiana
name: Uliano-Silva, Marcela
name: Van Den Beek, Marius
name: Williams, Robert W.
name: Waterhouse, Robert M.
name: Jarvis, Erich D.
name: Phillippy, Adam M.
name: Schatz, Michael
name: Formenti, Giulio
Publisher: name: F1000 Research Limited
Year: 2024

description: Recent improvements in genome sequencing and assembly promise to generate high-quality reference genomes for many species. Yet the genome assembly process is still laborious and costly, requires substantial expertise, and is generally not scalable to the goals of very large multispecies scientific efforts. To democratise the training and assembly process at scale, we continue to expand and improve the Vertebrate Genomes Project assembly pipeline in Galaxy, published earlier this year (Larivière et al. 2024). <br>
The automated pipeline performs <i>de novo</i> assembly based on PacBio HiFi reads, with optional extended graph phasing using Hi-C or parental data. It supports scaffolding using Bionano optical maps data and Hi-C via modular workflows. The workflows include quality control throughout the assembly process using GenomeScope, gfastats, Merqury, BUSCO, and Pretext.<br>
Within the Vertebrate Genome Project, these workflows have already been applied to <i>de novo</i> assemble genomes of over a hundred species, doubling the number of species reported in Larivière et al. 2024. We will present an overview of the new species assembled in Galaxy and what we learned from them. We will also present the updates to the published workflows and new workflows added to the VGP suite to assist with manual curation, including Galaxy workflow implementation producing most of the visualisation tracks from Treeval (Pointon, Eagles, and Sims, n.d.). <br>
The VGP's long-term goal is to use these workflows to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species, facilitating a new era of discovery across the life sciences. We will highlight how we use new developments in Planemo (Bray et al. 2023) to accelerate the production of genome assemblies through the command line. <br>
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Bray, Simon, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, et al. 2023. “The Planemo Toolkit for Developing, Deploying, and Executing Scientific Data Analyses in Galaxy and beyond.” <i>Genome Research</i> 33 (2): 261–68.<br>
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Larivière, Delphine, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, et al. 2024. “Scalable, Accessible and Reproducible Reference Genome Assembly and Evaluation in Galaxy.” <i>Nature Biotechnology</i>, January. https://doi.org/10.1038/s41587-023-02100-3.<br>
Pointon, D. L., W. Eagles, and Y. Sims. n.d. “Sanger-Tol/treeval v1. 0.0–Ancient Atlantis. 2023.” <i>Publisher Full Text</i>.