Nanopore sequencing : methods and protocols

Author(s)

    • Arakawa, Kazuharu

Bibliographic Information

Nanopore sequencing : methods and protocols

edited by Kazuharu Arakawa

(Methods in molecular biology / John M. Walker, series editor, 2632)(Springer protocols)

Humana Press, c2023

  • : [hbk]

Available at  / 3 libraries

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Note

Includes bibliographical references and index

Description and Table of Contents

Description

This volume provides comprehensive dry and wet experiments, methods, and applications on nanopore sequencing. Chapters guide readers through bioinformatic procedures, genome sequencing, analysis of repetitive regions, structural variations, rapid and on-site microbial identification, epidemiology, and transcriptome analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Nanopore Sequencing: Methods and Protocols aims to be comprehensive guide for researchers.

Table of Contents

Part I. Nanopore sequencing for genomics and beyond 1. The current state of nanopore sequencing Jonathan Pugh 2. Hybrid genome assembly of short and long reads in Galaxy Tazro Ohta and Yuh Shiwa 3. Microbial genome sequencing and assembly using nanopore sequencers, Makoto Taniguchi and Kazuma Uesaka 4. De novo genome assembly of Japanese Black cattle as model of an economically relevant animal Shinji Sasaki, Yasuhiko Haga, Hiroyuki Wakaguri, Kazumi Abe, and Yutaka Suzuki 5. How to sequence and assemble plant genomes Ken Naito 6. Detection of DNA modification using nanopore sequencers Yoshikazu Furuta 7. Ultra-low input genome library preparation for nanopore sequencing with droplet-MDA Kazuharu Arakawa 8. The method of eliminating the Wolbachia endosymbiont genomes from insect samples prior to long-reads Keizo Takasuka 9. A nanopore sequencing course for graduate school curriculum Kazuharu Arakawa Part II. Analysis of repetitive regions and structural variants 10. A guide to genome sequencing containing ultra-long repetitive regions Nobuaki Kono 11. Analysis of tandem repeat expansions using long DNA reads Satomi Mitsuhashi and Martin C Frith 12. Finding rearrangements in nanopore DNA reads with last and dnarrange Martin C. Frith and Satomi Mitsuhashi 13. Long read whole-genome sequencing using a nanopore sequencer and detection of structural variants in cancer genomes Yasuhiko Haga, Yoshitaka Sakamoto, Miyuki Arai, Yutaka Suzuki and Ayako Suzuki Part III. Rapid on-site microbial detection and epidemiology 14. Full-length 16S rRNA gene analysis using long-read nanopore sequencing for rapid identification of bacteria from clinical specimens Yoshiyuki Matsuo 15.Nanopore sequencing data analysis of 16S rRNA genes using Genome Sync-GSTK system Kirill Kryukov, Tadashi Imanishi and So Nakagawa 16. Genomic epidemiological analysis of antimicrobial-resistant bacteria with nanopore sequencing Masato Suzuki, Yusuke Hashimoto, Aki Hirabayashi, Koji Yahara, Mitsunori Yoshida, Hanako Fukano, Yoshihiko Hoshino, Keigo Shibayama, Haruyoshi Tomita 17. Rapid and comprehensive identification of nontuberculous mycobacteria, Yuki Matsumoto and Shota Nakamura Part IV. Nanopore sequencing for transcriptomics and beyond 18. Long-read single-cell sequencing using scCOLOR-seq Martin Philpott, Udo Oppermann and Adam P Cribbs 19. Unfolding the Bacterial Transcriptome Landscape using Oxford Nanopore Technology Direct RNA Sequencing Mohamad Al kadi and Daisuke Okuzaki 20. Nanopore Direct RNA Sequencing of Monosome-and Polysome-bound RNA Lan Anh Nguyen, Toshifumi Inada, and Josephine Galipon 21. RNA modification detection using nanopore direct RNA sequencing and nanoDoc2 Hiroki Ueda, Bhaskar Dasgupta, Bo-yi Yu

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Details

  • NCID
    BD02611612
  • ISBN
    • 9781071629956
  • Country Code
    us
  • Title Language Code
    eng
  • Text Language Code
    eng
  • Place of Publication
    New York
  • Pages/Volumes
    xi, 324 p.
  • Size
    27 cm
  • Classification
  • Subject Headings
  • Parent Bibliography ID
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