Nanopore Sequencing: Methods and Protocols

ISBN-13: 9781071629956 / Angielski / Twarda / 2023 / 334 str.

Kazuharu Arakawa

Opis

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.

Spis treści

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