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TECHNOLOGY AND CODE article

Front. Bioinform.
Sec. Genomic Analysis
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1462923

Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads

Provisionally accepted
Lia Obinu Lia Obinu 1*Urmi Trivedi Urmi Trivedi 2Andrea Porceddu Andrea Porceddu 1
  • 1 Department of Agricultural Sciences, University of Sassari, Sassari, Italy
  • 2 Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom

The final, formatted version of the article will be published soon.

    The implementation of Hi-C reads in the de novo genome assembly process allows the ordering of large regions of the genome in scaffolds and the generation of chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and each tool have advantages and disadvantages that need to be carefully evaluated before their adoption. We generated two de novo assemblies of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data. We scaffolded the assemblies implementing Hi-C reads with the scaffolders 3D-DNA, SALSA2, and YaHS, with the aim of identifying the tool providing the most accurate assembly. The scaffolded assemblies were evaluated according to contiguity, completeness, accuracy, and structural correctness.In our analysis, YaHS proved to be the best-performing bioinformatics tool for scaffolding of de novo genome assemblies in Arabidopsis thaliana.

    Keywords: Genome scaffolding, Hi-C reads, De novo genome assembly, AssemblyQC, Benchmarking

    Received: 10 Jul 2024; Accepted: 18 Oct 2024.

    Copyright: © 2024 Obinu, Trivedi and Porceddu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Lia Obinu, Department of Agricultural Sciences, University of Sassari, Sassari, Italy

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.