EndHiC

EndHiC scaffolds large contigs into chromosomal-level assemblies by using Hi-C links from contig end regions to improve signal-to-noise discrimination between adjacent and non-adjacent contigs.

Key Features:

• Contig end region focus: Uses Hi-C links specifically from contig end regions to enhance differentiation between adjacent (signal) and non-adjacent (noise) linkages.
• Reciprocal best requirement: Applies a reciprocal-best criterion to candidate scaffold joins.
• Robustness evaluation: Performs robustness evaluation of proposed joins to reduce mis-assembly.
• Accuracy for large contigs: Improves scaffolding accuracy for large contigs by concentrating on end-region Hi-C signals.
• Efficiency: Operates in a time-efficient and memory-friendly manner to limit computational resource usage.
• Broad applicability: Demonstrated across species including human, rice, Arabidopsis, great burdock, water spinach, chicory, endive, yacon, and Ipomoea cairica.

Scientific Applications:

• Chromosomal-level scaffolding of long-contig assemblies: Suited for assemblies with N50 near or exceeding 10 Mb and N90 near or over 1 Mb to achieve chromosomal-level scaffolds using Hi-C contacts.
• Cross-species genome assembly: Applicable to both plant and animal genomes as demonstrated in human, rice, Arabidopsis, great burdock, water spinach, chicory, endive, yacon, and Ipomoea cairica.

Methodology:

Extracts Hi-C links from contig end regions, applies a reciprocal-best requirement to candidate joins, and conducts robustness evaluation of proposed joins.