Robust long-read native DNA sequencing using the ONT CsgG Nanopore system Article Swipe
Jean-Michel Carter
,
Shobbir Hussain
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.12688/wellcomeopenres.11246.3
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.12688/wellcomeopenres.11246.3
Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements. Methods: We made use of such components on ONTs miniature ‘MinION’ device and sequenced native genomic DNA obtained from the near haploid cancer cell line HAP1. Analysis of our data was performed utilising recently described computational tools tailored for nanopore/long-read sequencing outputs, and here we present our key findings. Results: From a single sequencing run, we obtained ~240,000 high-quality mapped reads, comprising a total of ~2.3 billion bases. A mean read length of 9.6kb and an N50 of ~17kb was achieved, while sequences mapped to reference with a mean identity of 85%. Notably, we obtained ~68X coverage of the mitochondrial genome and were able to achieve a mean consensus identity of 99.8% for sequenced mtDNA reads. Conclusions: With improved sequencing chemistries already released and higher-throughput instruments in the pipeline, this early study suggests that ONT CsgG-based sequencing may be a useful option for potential practical long-read applications with relevance to complex genomes.
Related Topics
Concepts
Nanopore sequencing
Minion
Biology
Reference genome
DNA sequencing
Computational biology
Structural variation
Genomics
Genome
Pipeline (software)
Genetics
Computer science
DNA
Gene
Programming language
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.12688/wellcomeopenres.11246.3
- OA Status
- gold
- Cited By
- 44
- References
- 34
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2605196606
All OpenAlex metadata
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https://openalex.org/W2605196606Canonical identifier for this work in OpenAlex
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https://doi.org/10.12688/wellcomeopenres.11246.3Digital Object Identifier
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Robust long-read native DNA sequencing using the ONT CsgG Nanopore systemWork title
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preprintOpenAlex work type
- Language
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enPrimary language
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2018Year of publication
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2018-08-30Full publication date if available
- Authors
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Jean-Michel Carter, Shobbir HussainList of authors in order
- Landing page
-
https://doi.org/10.12688/wellcomeopenres.11246.3Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.12688/wellcomeopenres.11246.3Direct OA link when available
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Nanopore sequencing, Minion, Biology, Reference genome, DNA sequencing, Computational biology, Structural variation, Genomics, Genome, Pipeline (software), Genetics, Computer science, DNA, Gene, Programming languageTop concepts (fields/topics) attached by OpenAlex
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44Total citation count in OpenAlex
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2025: 1, 2024: 1, 2023: 2, 2022: 4, 2021: 11Per-year citation counts (last 5 years)
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34Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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