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

• Published in: Genomics (San Diego, Calif.) Calif.), 2023-09, Vol.115 (5), p.110700-110700, Article 110700
• Main Authors: Espinosa, Elena, Bautista, Rocio, Fernandez, Ivan, Larrosa, Rafael, Zapata, Emilio L., Plata, Oscar
• Format: Article
• Language: English
• Subjects: data collection; genome; Genome assembly; genomics; haplotypes; HiFi; Hybrid assembly; hybrids; nanopores; ONT; PacBio
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2023.110700

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. •This study evaluates the assembly of the genome of different organisms from hybrid and non-hybrid strategies of assembly.•Assembly using HiFi reads yields genome sequences that are more continuous and complete while being cost-effective.•Through hybrid assembly, the number of translocations can be reduced, thereby increasing genome correctness.