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Updated: May 29, 2026
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
Song Gao1, Wing-Kin Sung, Niranjan Nagarajan
1NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
Summary
Opera provides the first tractable, exact solution for genome assembly scaffolding, improving contig ordering and orientation. This approach yields longer, more accurate scaffolds compared to heuristic methods.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome assembly relies on scaffolding to order and orient DNA contigs.
- Current scaffolding methods use heuristics with no quality guarantees.
- Advancements in sequencing technologies necessitate improved scaffolding solutions.
Purpose of the Study:
- To explore the feasibility of an exact solution for genome scaffolding.
- To introduce Opera, a novel scaffolding tool based on an exact approach.
- To develop a scalable method for large-scale genome assembly.
Main Methods:
- Developed a novel exact algorithm for the scaffolding problem.
- Implemented a graph contraction procedure for scalability.
- Utilized an exact quadratic programming formulation for gap size computation.
Main Results:
- Opera successfully scaffolded large real and synthetic datasets.
- Opera produced longer and more accurate scaffolds than existing methods.
- Demonstrated the utility and scalability of an exact approach to scaffolding.
Conclusions:
- An exact approach is feasible and beneficial for genome scaffolding.
- Opera offers a significant improvement over heuristic scaffolding methods.
- The developed method provides accurate gap size computation for genome assembly.
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03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
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