<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>The assembly of billions of short sequencing reads into a contiguous genome is a daunting task. The foundation knowledge of current DNA assembly models is concentrated among a select group, where the solution to the genome assembly challenge lies in proper ordering the genomic data. This contribution’s objective is to provide an overview of the original graph models used in DNA sequencing by hybridization. With the updated analytical approach based on the bidirectional bipartite graph class, the theoretical basic structure of the DNA assembly model has been described in new perspective by incorporating few short hypothetical DNA sequences. On the Galaxy platform, by using Spades assembler and Velvet assembler, the comparative outcomes of an experiment are presented, and we also identify their working schemes. Here, the working principle of de Bruijn graph has been discussed in broader point of view.</p>
</abstract>

The assembly of billions of short sequencing reads into a contiguous genome is a daunting task. The foundation knowledge of current DNA assembly models is concentrated among a select group, where the solution to the genome assembly challenge lies in proper ordering the genomic data. This contribution’s objective is to provide an overview of the original graph models used in DNA sequencing by hybridization. With the updated analytical approach based on the bidirectional bipartite graph class, the theoretical basic structure of the DNA assembly model has been described in new perspective by incorporating few short hypothetical DNA sequences. On the Galaxy platform, by using Spades assembler and Velvet assembler, the comparative outcomes of an experiment are presented, and we also identify their working schemes. Here, the working principle of de Bruijn graph has been discussed in broader point of view.

A Study of Computational Genome Assembly by Graph Theory

Department of Mathematics Neotia Institute of Technology

Annals of West University of Timisoara - Mathematics and Computer Science

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

{"article-title":"A Study of Computational Genome Assembly by Graph Theory"}

The assembly of billions of short sequencing reads into a contiguous genome is a daunting task. The foundation knowledge of current DNA assembly models is...

A Study of Computational Genome Assembly by Graph Theory

Published Online: Feb 24, 2024

Page range: 1 - 24

Received: Feb 07, 2023

Accepted: Feb 13, 2024

DOI: https://doi.org/10.2478/awutm-2024-0001

Keywords
Genome assembly, De novo assembly, De Bruijn graphs, Bidirectional bipartite graphs, Spades assembler, Velvet assembler

© 2024 Bijan Sarkar, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

A Study of Computational Genome Assembly by Graph Theory

Published Online: Feb 24, 2024

Page range: 1 - 24

Received: Feb 07, 2023

Accepted: Feb 13, 2024

DOI: https://doi.org/10.2478/awutm-2024-0001

KeywordsGenome assembly, De novo assembly, De Bruijn graphs, Bidirectional bipartite graphs, Spades assembler, Velvet assembler

© 2024 Bijan Sarkar, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
Genome assembly, De novo assembly, De Bruijn graphs, Bidirectional bipartite graphs, Spades assembler, Velvet assembler