Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction Article Swipe
Xuyang Zhao
,
Junyao Li
,
Qingyuan Fan
,
Jing Dai
,
Yanping Long
,
Ronghui Liu
,
Jixian Zhai
,
Qing Pan
,
Yi Li
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-024-53455-3
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-024-53455-3
Reading digital information from highly dense but lightweight DNA medium nowadays relies on time-consuming next-generation sequencing. Nanopore sequencing holds the promise to overcome the efficiency problem, but high indel error rates lead to the requirement of large amount of high quality data for accurate readout. Here we introduce Composite Hedges Nanopores, capable of handling indel rates up to 15.9% and substitution rates up to 7.8%. The overall information density can be doubled from 0.59 to 1.17 by utilizing a degenerated eight-letter alphabet. We demonstrate that sequencing times of 20 and 120 minutes are sufficient for processing representative text and image files, respectively. Moreover, to achieve complete data recovery, it is estimated that text and image data require 4× and 8× physical redundancy of composite strands, respectively. Our codec system excels on both molecular design and equalized dictionary usage, laying a solid foundation approaching to real-time DNA data retrieval and encoding.
Related Topics
Concepts
Indel
Nanopore sequencing
DNA
Nanopore
Codec
Computer science
Computational biology
Genetics
Nanotechnology
Biology
Materials science
DNA sequencing
Computer hardware
Genotype
Gene
Single-nucleotide polymorphism
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41467-024-53455-3
- OA Status
- gold
- Cited By
- 11
- References
- 44
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403921251
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4403921251Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s41467-024-53455-3Digital Object Identifier
- Title
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Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-CorrectionWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-10-30Full publication date if available
- Authors
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Xuyang Zhao, Junyao Li, Qingyuan Fan, Jing Dai, Yanping Long, Ronghui Liu, Jixian Zhai, Qing Pan, Yi LiList of authors in order
- Landing page
-
https://doi.org/10.1038/s41467-024-53455-3Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://doi.org/10.1038/s41467-024-53455-3Direct OA link when available
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Indel, Nanopore sequencing, DNA, Nanopore, Codec, Computer science, Computational biology, Genetics, Nanotechnology, Biology, Materials science, DNA sequencing, Computer hardware, Genotype, Gene, Single-nucleotide polymorphismTop concepts (fields/topics) attached by OpenAlex
- Cited by
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11Total citation count in OpenAlex
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2025: 9, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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44Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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