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bio-genome-assembly-scaffolding

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Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, and SALSA2, and validate with BUSCO and contact maps.

When to use

• Scaffolding contigs to chromosome-level assemblies
• Hi-C data preprocessing
• YaHS scaffolding
• 3D-DNA pipeline execution
• SALSA2 scaffolding
• Generating contact maps
• Visualizing with HiGlass
• Manual curation with Juicebox

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