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bioRxiv · 10.64898/2026.07.17.739168

Hobrac: a reference-guided workflow for genome comparison and synteny visualization

Istace, B.·Denoeud, F.·Teodori, E.·Chorba, N.·Aury, J.-M.
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Abstract

Whole-genome comparison is fundamental for validating genome assemblies and investigating genome evolution, yet identifying suitable reference genomes and interpreting chromosome-scale synteny from often noisy nucleotide alignments remain challenging. We introduce Hobrac, an automated workflow that addresses these two major bottlenecks by combining automated reference genome selection with gene-based structural comparisons. Starting from a genome assembly and its taxon identifier, Hobrac identifies suitable reference genomes, complements nucleotide alignments with conserved BUSCO orthologues, and generates publication-quality visualizations. The workflow produces dotplots, ribbon-plots and synteny visualization that can be explored interactively or offline. Hobrac is freely available at https://github.com/Genoscope-LBGB/hobrac.

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Istace, B., Denoeud, F., Teodori, E., Chorba, N., Aury, J.-M.. 2026-07-22. Hobrac: a reference-guided workflow for genome comparison and synteny visualization. https://doi.org/10.64898/2026.07.17.739168

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