HiRise

HiRise produces long-range, highly contiguous genome scaffolds from short-read sequencing data by using proximity ligation on in vitro reconstituted chromatin (Chicago libraries) combined with statistical modeling to improve de novo and existing assemblies.

Key Features:

• Identification of Poor Quality Joins: Detects and removes suboptimal joins in assemblies to prevent incorrect scaffold connections.
• Production of Long-Range Sequence Scaffolds: Generates long-range scaffolds using proximity ligation of DNA within in vitro reconstituted chromatin to create long-range read pairs.
• Statistical Modeling and Pipeline: Implements a statistical model and processing pipeline tailored for data from Chicago libraries.
• Application to Human Genome Assembly: Produced a human de novo assembly with a scaffold N50 of 20 Mbp.
• Improvement of Existing Assemblies: Increased the American alligator scaffold N50 from 508 kbp to 10 Mbp using a single Chicago library and one lane of Illumina HiSeq sequencing.

Scientific Applications:

• De novo Genome Assembly: Enhances contiguity and accuracy of de novo genome assemblies from short-read sequencing data.
• Assembly Refinement and Scaffolding: Refines existing assemblies to increase scaffold N50 and long-range contiguity.
• Comparative Genomics and Evolutionary Biology: Enables generation of more contiguous assemblies for comparative and evolutionary analyses, and supports applications relevant to personalized medicine.

Methodology:

Processes proximity-ligation data from Chicago libraries using a statistical model to detect and remove poor-quality joins and scaffold assemblies into long-range contigs.