Comparing assembly strategies for third-generation sequencing technologies across different genomes

Elena Espinosa; Rocio Bautista; Ivan Fernandez; Rafael Larrosa; Emilio L Zapata; Oscar Plata

doi:10.1016/j.ygeno.2023.110700

Comparing assembly strategies for third-generation sequencing technologies across different genomes

Genomics. 2023 Sep;115(5):110700. doi: 10.1016/j.ygeno.2023.110700. Epub 2023 Aug 18.

Authors

Elena Espinosa¹, Rocio Bautista², Ivan Fernandez³, Rafael Larrosa⁴, Emilio L Zapata⁵, Oscar Plata⁶

Affiliations

¹ Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain. Electronic address: elenamesga@uma.es.
² Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain. Electronic address: rociobm@uma.es.
³ Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Departament d'Arquitectura de Computadors, Universitat Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona 08034, Spain. Electronic address: ivanfv@uma.es.
⁴ Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain. Electronic address: rlarrosa@uma.es.
⁵ Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain. Electronic address: ezapata@ac.uma.es.
⁶ Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain. Electronic address: oplata@uma.es.

PMID: 37598732
DOI: 10.1016/j.ygeno.2023.110700

Abstract

The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.

Keywords: Genome assembly; HiFi; Hybrid assembly; ONT; PacBio.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome*
High-Throughput Nucleotide Sequencing* / methods
Sequence Analysis, DNA / methods