Open Access

Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly

  • Authors:
    • Marios Gavrielatos
    • Konstantinos Kyriakidis
    • Demetrios A. Spandidos
    • Ioannis Michalopoulos
  • View Affiliations

  • Published online on: February 2, 2021     https://doi.org/10.3892/mmr.2021.11890
  • Article Number: 251
  • Copyright: © Gavrielatos et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )


Abstract

Genome assemblers are computational tools for de novo genome assembly, based on a plenitude of primary sequencing data. The quality of genome assemblies is estimated by their contiguity and the occurrences of misassemblies (duplications, deletions, translocations or inversions). The rapid development of sequencing technologies has enabled the rise of novel de novo genome assembly strategies. The ultimate goal of such strategies is to utilise the features of each sequencing platform in order to address the existing weaknesses of each sequencing type and compose a complete and correct genome map. In the present study, the hybrid strategy, which is based on Illumina short paired‑end reads and Nanopore long reads, was benchmarked using MaSuRCA and Wengan assemblers. Moreover, the long‑read assembly strategy, which is based on Nanopore reads, was benchmarked using Canu or PacBio HiFi reads were benchmarked using Hifiasm and HiCanu. The assemblies were performed on a computational cluster with limited computational resources. Their outputs were evaluated in terms of accuracy and computational performance. PacBio HiFi assembly strategy outperforms the other ones, while Hi‑C scaffolding, which is based on chromatin 3D structure, is required in order to increase continuity, accuracy and completeness when large and complex genomes, such as the human one, are assembled. The use of Hi‑C data is also necessary while using the hybrid assembly strategy. The results revealed that HiFi sequencing enabled the rise of novel algorithms which require less genome coverage than that of the other strategies making the assembly a less computationally demanding task. Taken together, these developments may lead to the democratisation of genome assembly projects which are now approachable by smaller labs with limited technical and financial resources.
View Figures
View References

Related Articles

Journal Cover

April-2021
Volume 23 Issue 4

Print ISSN: 1791-2997
Online ISSN:1791-3004

Sign up for eToc alerts

Recommend to Library

The Cancer Story
Copy and paste a formatted citation
x
Spandidos Publications style
Gavrielatos M, Kyriakidis K, Spandidos DA and Michalopoulos I: Benchmarking of next and third generation sequencing technologies and their associated algorithms for <em>de novo</em> genome assembly. Mol Med Rep 23: 251, 2021
APA
Gavrielatos, M., Kyriakidis, K., Spandidos, D.A., & Michalopoulos, I. (2021). Benchmarking of next and third generation sequencing technologies and their associated algorithms for <em>de novo</em> genome assembly. Molecular Medicine Reports, 23, 251. https://doi.org/10.3892/mmr.2021.11890
MLA
Gavrielatos, M., Kyriakidis, K., Spandidos, D. A., Michalopoulos, I."Benchmarking of next and third generation sequencing technologies and their associated algorithms for <em>de novo</em> genome assembly". Molecular Medicine Reports 23.4 (2021): 251.
Chicago
Gavrielatos, M., Kyriakidis, K., Spandidos, D. A., Michalopoulos, I."Benchmarking of next and third generation sequencing technologies and their associated algorithms for <em>de novo</em> genome assembly". Molecular Medicine Reports 23, no. 4 (2021): 251. https://doi.org/10.3892/mmr.2021.11890