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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Updated: Jun 28, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing.

Yibo Chen¹, Jun-Han Huang¹, Yuhui Sun¹

¹BGI Research, Shenzhen 518083, China.

Cell Reports Methods

|April 13, 2024

Summary

Quantum computing offers new solutions for haplotype-resolved genome assembly, a key challenge in precision medicine. This study introduces a quantum approach, demonstrating its potential for accurate genetic variant analysis.

Keywords:

CP: Genetics bioinformatics haplotype assembly polyploid genome assembly quantum annealing quantum computing application quantum life sciences quantum optimization vehicle routing problem

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Last Updated: Jun 28, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Bioinformatics
Computational Biology
Quantum Computing

Background:

Precision medicine relies on understanding individual genetic variants.
Haplotype-resolved assembly is crucial but computationally challenging.
Classical algorithms have limitations, and quantum computing's potential is underexplored.

Purpose of the Study:

To develop a novel computational approach for haplotype-resolved assembly using quantum computing.
To transform the assembly problem into a vehicle routing problem (VRP) solvable on quantum hardware.
To assess the feasibility and performance of this quantum-inspired method.

Main Methods:

Formulated haplotype-resolved assembly as a vehicle routing problem.
Utilized a D-Wave quantum annealer for proof-of-concept on synthetic genomes.
Integrated the VRP assembler with Google's OR-Tools for larger-scale applications.
Applied the method to the human major histocompatibility complex (MHC) region.

Main Results:

Demonstrated proof-of-concept on short synthetic diploid and triploid genomes.
Achieved haplotype-resolved local assembly in the human MHC region.
Showed encouraging performance and phasing accuracy comparable to state-of-the-art classical methods (Hifiasm).

Conclusions:

The VRP assembler approach shows promise for accurate haplotype-resolved genome assembly.
Quantum computing offers a viable and powerful avenue for tackling complex bioinformatics challenges.
This work highlights the potential of quantum algorithms in advancing precision medicine and genomics.