SYSTEMATIC COMPARISON OF COMPUTATIONAL PIPELINES FOR EUKARYOTIC GENOME ASSEMBLY USING OXFORD NANOPORE TECHNOLOGY DATA

Lucas Silveira Veiga; Yago Mendes Paes; Karina Machado; Adriano Werhli

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Submission

Paper Title

SYSTEMATIC COMPARISON OF COMPUTATIONAL PIPELINES FOR EUKARYOTIC GENOME ASSEMBLY USING OXFORD NANOPORE TECHNOLOGY DATA

Authors

Lucas Silveira Veiga
Yago Mendes Paes
Karina Machado
Adriano Werhli

Modality

Poster

Subject area

DNA and Genomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/836510-systematic-comparison-of-computational-pipelines-for-eukaryotic-genome-assembly-using-oxford-nanopore-technology-

ISBN

978-65-272-0843-3

Keywords

Next-Generation Sequencing, Genome Assembly, Bioinformatics, Basecalling

Summary

DNA sequencing technologies are of paramount importance as they are related to various fields such as clinical research, where they are used to diagnose genetic diseases and discover genes and their functions, and biodiversity conservation, where they are used in phylogeny and evolutionary studies. Next-generation sequencing technologies (NGS) represent the latest advances in DNA sequencing, overcoming the limitations of previous generations that yielded only short-read sequences, while NGS offers long-read sequencing capabilities that enable the analysis of significantly larger DNA fragments compared to earlier methods. As a result, NGS has made it much more feasible to assemble large genomes, such as those of eukaryotic organisms. Genome assembly is generally complex due to the many variables involved, such as the amount of repetitive sequences within the genome. In the case of eukaryotic genomes, the complexity is increased due to the size and organization of the chromosomes, including telomeres and centromeres. Oxford Nanopore Technology (ONT), a form of long-read sequencing technology, is one of the most important NGS technologies. ONT is based on nanopore technology, in which a single-stranded DNA molecule is passed through a nanopore and changes in electrical current are measured to determine the sequence bases. This technology is widely used in various areas of omics and generates massive amounts of data extremely quickly. As these data are generated, various computational methods related to bioinformatics are being developed, specialized tools that aim to optimize and accurately perform each phase of processing these data. Given the amount of options, researchers must select the most suitable assembly tools for their project. For that reason, it is important to establish a workflow that incorporates the most efficient tools for each phase of genome assembly. This study aims to systematically compare computational pipelines for genome assembly from nanopore sequencing data sourced from the Oxford Nanopore Open Data Project platform. By investigating various methods, tools, and parameters for basecalling, pre-processing, quality control and assembly, we propose to elucidate optimal strategies for genome construction of eukaryotic organisms. Our aim is to devise pipelines that take into account the distinct stages of nanopore sequencing and the computational challenges associated with the assembly of eukaryotic genomes by evaluating the effectiveness of different computational tools and parameters in the assembly of their genomes, in terms of quality, contiguity, precision and coverage. ONT provides its users through EPI2ME Lab, an interactive platform, the possibility of analyzing their own data in an intuitive way, offering workflows for various analyses. It also offers Dorado, an open source basecaller, specialized for nanopore reads. Thus, we will compare the ONT platform EPI2ME Labs and Dorado software with the most cited software in the literature for the analysis of: (i) Basecalling (Read-Until, DeepNano, Chiron), (ii) Alignment (Starlong, Minimap2, LAST) and (iii) Quality Trimming (Canu, NanoFilt, SQANTI3). By conducting this analysis, we aim to compare different approaches and determine the most suitable pipeline options for each scenario, improving the operational methodology to optimize the utilization of these tools.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

VEIGA, Lucas Silveira et al.. SYSTEMATIC COMPARISON OF COMPUTATIONAL PIPELINES FOR EUKARYOTIC GENOME ASSEMBLY USING OXFORD NANOPORE TECHNOLOGY DATA.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/836510-SYSTEMATIC-COMPARISON-OF-COMPUTATIONAL-PIPELINES-FOR-EUKARYOTIC-GENOME-ASSEMBLY-USING-OXFORD-NANOPORE-TECHNOLOGY-. Access in: 06/06/2025