Opera

Opera performs scaffolding in genome assembly by ordering and orienting contigs using paired-end read information from shotgun sequencing reads to construct high-quality draft genomes.

Key Features:

• Exact quadratic programming formulation: Uses a quadratic programming model to compute gap sizes between contigs precisely.
• Graph contraction procedure: Employs a novel graph contraction method to reduce problem complexity and enable efficient processing of large scaffolding graphs.
• Paired-end read utilization: Integrates paired-end read information to determine contig order and orientation.
• Gap size computation: Precisely estimates inter-contig gap sizes as part of scaffold construction.
• Scalability: Designed to handle large-scale scaffolding tasks through algorithmic contraction and exact optimization.
• Improved scaffold quality: Produces longer and more accurate scaffolds compared to existing heuristic scaffolders.

Scientific Applications:

• Draft genome construction: Scaffolding contigs to assemble high-quality draft genomes from shotgun sequencing data.
• Large-scale genome projects: Applying scalable scaffolding to large datasets and complex assemblies.
• Benchmarking and validation: Comparative analyses and validation on real and synthetic datasets to assess scaffold accuracy and performance.

Methodology:

Opera implements an exact solution to scaffolding by combining a novel graph contraction procedure with an exact quadratic programming formulation to compute gap sizes using paired-end read information.