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A Guide to Sequencing for Long Repetitive Regions

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Nanopore Sequencing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2632))

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Abstract

Full-length analysis of genes with highly repetitive sequences is challenging in two respects: assembly algorithm and sequencing accuracy. The de Bruijn graph often used in short-read assembly cannot distinguish adjacent repeat units. On the other hand, the accuracy of long reads is not yet high enough to identify each and every repeat unit. In this chapter, I present an example of a strategy to solve these problems and obtain the full length of long repeats by combining the extraction and assembly of repeat units based on overlap-layout-consensus and scaffolding by long reads.

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References

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Authors and Affiliations

  1. Institute for Advanced Biosciences, Keio University, Tsuruoka City, Yamagata, Japan

    Nobuaki Kono

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  1. Nobuaki Kono
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Correspondence to Nobuaki Kono .

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Editors and Affiliations

  1. Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

    Kazuharu Arakawa

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Kono, N. (2023). A Guide to Sequencing for Long Repetitive Regions. In: Arakawa, K. (eds) Nanopore Sequencing. Methods in Molecular Biology, vol 2632. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2996-3_10

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  • DOI: https://doi.org/10.1007/978-1-0716-2996-3_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2995-6

  • Online ISBN: 978-1-0716-2996-3

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