pin_hic

pin_hic constructs chromosome-scale genome scaffolds from Hi-C sequencing data by leveraging chromosomal contact information to improve continuity and accuracy of de novo assemblies.

Key Features:

• Iterative scaffolding graph construction: Constructs a scaffolding graph iteratively using N-best neighbors from contigs to integrate Hi-C contact data for scaffold ordering and orientation.
• Hi-C contact integration: Leverages chromosomal contact information captured by Hi-C reads to inform contig linking and scaffold continuity.
• Misjoin identification and correction: Identifies potential misjoins within scaffolds and breaks them to maintain assembly fidelity.
• Chromosome-number agnostic scaffolding: Operates without requiring prior knowledge of chromosome numbers when building scaffolds.
• Performance on long-read assemblies: Demonstrated improved scaffold continuity and comparable or higher accuracy on de novo assemblies from three species using long-read sequencing data.

Scientific Applications:

• Chromosome-scale genome assembly: Produces chromosome-scale scaffolds from fragmented contigs using Hi-C contact information.
• Scaffolding de novo assemblies: Enhances continuity and accuracy of assemblies generated from long-read sequencing technologies.
• Application across eukaryotes: Applicable to assembling genomes of diverse eukaryotic species, including cases where chromosome number is unknown.

Methodology:

Organizes contigs into scaffolds via an iterative scaffolding graph built from N-best neighbors derived from Hi-C contact data and detects and breaks misjoins.