allhic

allhic constructs chromosome‑level, allele‑aware genome assemblies by leveraging Hi‑C data to scaffold and phase allelic contigs in autopolyploid, allopolyploid, and highly heterozygous genomes.

Key Features:

• Allele‑Aware Assembly: Constructs chromosomal‑scale, allele‑aware assemblies that distinguish alleles in autopolyploid genomes.
• Hi‑C‑Based Scaffolding: Leverages high‑throughput chromosome conformation capture (Hi‑C) data to group, scaffold, and orient contigs into chromosomes.
• Prune and Optimize Steps: Incorporates explicit "prune" and "optimize" algorithmic steps to refine assemblies, phase allelic contigs, and improve ordering and orientation.
• Phasing of Allelic Contigs: Phases allelic contigs to represent allelic variation within assembled chromosomes.
• Support for Complex Genomes: Applies to autopolyploid, allopolyploid, and highly heterozygous diploid genomes, including autotetraploid and autooctoploid cases.
• Performance Validation: Demonstrated superior performance on simulated datasets relative to other mainstream Hi‑C assemblers.
• Real‑World Applications: Applied to construct phased chromosomal‑level assemblies for sugar‑cane (autotetraploid and autooctoploid), revealing allelic variation.

Scientific Applications:

• Genome Assembly: Enables de novo chromosome‑level assembly of complex and polyploid genomes using Hi‑C data.
• Genetic Variation Analysis: Separates and phases alleles during assembly to enable study of allelic variation and genome structure.
• Crop Genomics and Improvement: Facilitates construction of phased assemblies in crop species (e.g., sugar‑cane) to inform breeding and genetic studies.

Methodology:

Uses Hi‑C contact information to group and scaffold contigs and implements explicit "prune" and "optimize" algorithmic steps to phase allelic contigs and determine ordering and orientation.