Nanopore Sequencing, 1st ed. 2023
Methods and Protocols
Methods in Molecular Biology Series, Vol. 2632

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.

Part I. Nanopore sequencing for genomics and beyond

1. The current state of nanopore sequencing

Jonathan Pugh

Tazro Ohta and Yuh Shiwa

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

Ken Naito

6. Detection of DNA modification using nanopore sequencers

7. Ultra-low input genome library preparation for nanopore sequencing with droplet-MDA

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

Nobuaki Kono

Satomi Mitsuhashi and Martin C Frith

12. Finding rearrangements in nanopore DNA reads with last and dnarrange

Martin C. Frith and Satomi Mitsuhashi

Yasuhiko Haga, Yoshitaka Sakamoto, Miyuki Arai, Yutaka Suzuki and Ayako Suzuki

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

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

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

Hiroki Ueda, Bhaskar Dasgupta, Bo-yi Yu

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts