Do we still need Illumina sequencing data?: Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and v14 library prep kits for Gram negative bacteria whole genome assemblies
Canadian Journal of Microbiology(2023)
摘要
The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher-quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we were interested in evaluating how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30X long-read coverage is sufficient if Illumina data is available, and that 100X long-read coverage is recommended for long-read-only assemblies. We found that Illumina polishing is still improving SNVs and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected > 94 % of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy depending on the specific use case and resources available.
### Competing Interest Statement
The authors have declared no competing interest.
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