LACHESIS

LACHESIS scaffolds de novo genome assemblies to chromosome scale by leveraging Hi-C chromatin contact probability maps to assign, order, and orient scaffolds.

Key Features:

• Utilization of Hi-C Data: Uses genome-wide Hi-C chromatin interaction (contact probability) maps to provide long-range linkage information for scaffold assignment, ordering, and orientation, including across centromeres.
• Ultra-Long-Range Scaffolding: Implements an algorithm that integrates shotgun fragment sequences, short jump mate-pair sequences, and Hi-C data for ultra-long-range scaffolding.
• High Accuracy in Assembly: Reports 98% accuracy in assigning scaffolds to chromosome groups and 99% accuracy in ordering and orienting scaffolds within groups on the human genome.
• Applications Across Species: Has been applied to generate chromosome-scale de novo assemblies for human, mouse, and Drosophila genomes.
• Validation of Chromosomal Translocations: Can validate chromosomal translocations in cancer genomes by analyzing Hi-C interaction patterns.

Scientific Applications:

• Chromosome-scale de novo assembly: Enables construction of chromosome-scale assemblies by integrating Hi-C with shotgun and mate-pair sequencing data.
• Cancer genomics: Supports validation of structural variations, including chromosomal translocations, in cancer genomes using Hi-C data.
• Cross-species genome assembly: Facilitates generation of high-contiguity assemblies across diverse species such as human, mouse, and Drosophila.

Methodology:

Integrates Hi-C contact probability maps with shotgun fragment and short jump mate-pair sequences via an algorithm that assigns scaffolds to chromosome groups and orders and orients them within each group.