Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2 Article Swipe
Alexander Zee
,
Dori Z.Q. Deng
,
Matthew S. Adams
,
Kayla D. Schimke
,
Russell Corbett‐Detig
,
Shelbi L. Russell
,
Xuan Zhang
,
Robert J. Schmitz
,
Christopher Vollmers
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/gr.277031.122
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/gr.277031.122
High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short-read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the rolling circle to concatemeric consensus (R2C2) method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, and regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.
Related Topics
Concepts
Minion
Nanopore sequencing
Illumina dye sequencing
DNA sequencer
DNA sequencing
Biology
Computational biology
Hybrid genome assembly
Deep sequencing
Computer science
Genetics
Genome
DNA
Shotgun sequencing
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/gr.277031.122
- https://genome.cshlp.org/content/32/11-12/2092.full.pdf
- OA Status
- hybrid
- Cited By
- 23
- References
- 49
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4308654983
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4308654983Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/gr.277031.122Digital Object Identifier
- Title
-
Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2Work title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
-
2022-11-01Full publication date if available
- Authors
-
Alexander Zee, Dori Z.Q. Deng, Matthew S. Adams, Kayla D. Schimke, Russell Corbett‐Detig, Shelbi L. Russell, Xuan Zhang, Robert J. Schmitz, Christopher VollmersList of authors in order
- Landing page
-
https://doi.org/10.1101/gr.277031.122Publisher landing page
- PDF URL
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https://genome.cshlp.org/content/32/11-12/2092.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://genome.cshlp.org/content/32/11-12/2092.full.pdfDirect OA link when available
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Minion, Nanopore sequencing, Illumina dye sequencing, DNA sequencer, DNA sequencing, Biology, Computational biology, Hybrid genome assembly, Deep sequencing, Computer science, Genetics, Genome, DNA, Shotgun sequencing, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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23Total citation count in OpenAlex
- Citations by year (recent)
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2025: 3, 2024: 8, 2023: 12Per-year citation counts (last 5 years)
- References (count)
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49Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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