The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

Cook, Ryan; Brown, Nathan; Rihtman, Branko; Michniewski, Slawomir; Redgwell, Tamsin; Clokie, Martha; Stekel, Dov J.; Chen, Yin; Scanlan, David J.; Hobman, Jon L.; Nelson, Andrew; Jones, Michael A.; Smith, Darren; Millard, Andrew

Abstract

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Citation

Cook, R., Brown, N., Rihtman, B., Michniewski, S., Redgwell, T., Clokie, M., …Millard, A. (2024). The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microbial Genomics, 10(2), Article 0.001198. https://doi.org/10.1099/mgen.0.001198

• Journal Article Type: Article
• Acceptance Date: Jan 25, 2024
• Online Publication Date: Apr 20, 2024
• Publication Date: Feb 20, 2024
• Deposit Date: Mar 18, 2024
• Publicly Available Date: Mar 19, 2024
• Journal: Microbial Genomics
• Electronic ISSN: 2057-5858
• Publisher: Microbiology Society
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Issue: 2
• Article Number: 0.001198
• DOI: https://doi.org/10.1099/mgen.0.001198
• Keywords: bacteriophage, bioinformatics, hybrid assembly, Illumina, long-reads, Nanopore, PacBio, Phage, viral metagenomics, Viromics
• Public URL: https://nottingham-repository.worktribe.com/output/31618855
• Publisher URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001198