YaHS

YaHS constructs chromosome-scale scaffolds from Hi-C data to produce high-contiguity genome assemblies.

Key Features:

• Hi-C-based scaffolding: Uses Hi-C interaction data to assemble contigs into chromosome-scale scaffolds.
• Contig-joining detection algorithm: A novel algorithm analyzes the topological distribution of Hi-C signals to detect contig joins and distinguish genuine interactions from mapping noise.
• Inputs: Accepts an assembly file and an alignment file compatible with similar tools.
• Implementation: Implemented in C for computational efficiency and scalability.
• Outputs: Produces assembly results in multiple file formats.

Scientific Applications:

• Chromosome-scale genome assembly: Construction of chromosome-scale scaffolds from Hi-C data.
• Scaffold improvement: Improving scaffold contiguity and accuracy by discriminating true interaction signals from mapping noise.
• Large-scale genomics: Applicable to large-scale genomic projects requiring efficient scaffolding of assemblies.
• Downstream integration: Generation of assemblies suitable for integration into downstream analyses or pipelines.

Methodology:

A novel contig-joining detection algorithm analyzes the topological distribution of Hi-C signals to distinguish genuine interactions from mapping noise; the software is implemented in C and operates on an assembly file and an alignment file to produce assembly outputs in multiple formats.