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Metagenomic Data Analysis

  • Book
  • © 2023

Overview

Editors:
  1. Suparna Mitra

    1. Leeds Institute of Medical Research, University of Leeds, Leeds, UK

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2649)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. From Genomics to Metagenomics in the Era of Recent Sequencing Technologies

    • Saskia Benz, Suparna Mitra
    Pages 1-20

  3. Quality Control in Metagenomics Data

    • Abraham Gihawi, Ryan Cardenas, Rachel Hurst, Daniel S. Brewer
    Pages 21-54

  4. Metagenomics Databases for Bacteria

    • Dapeng Wang
    Pages 55-67

  5. Amplicon Sequencing Pipelines in Metagenomics

    • Dapeng Wang
    Pages 69-83

  6. A Practical Guide to 16S rRNA Microbiome Analysis in Musculoskeletal Disorders

    • C. M. Rooney, S. Mitra
    Pages 85-105

  7. DIAMOND +  MEGAN Microbiome Analysis

    • Anupam Gautam, Wenhuan Zeng, Daniel H. Huson
    Pages 107-131

  8. Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons

    • Nehal Adel Abdelsalam, Hajar Elshora, Mohamed El-Hadidi
    Pages 133-174

  9. Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST

    • Ramitha Arumugam, Prithivan Ravichandran, Swee Keong Yeap, Reuben Sunil Kumar Sharma, Shahrizim Bin Zulkifly, Donny Yawah et al.
    Pages 175-194

  10. Designing Knowledge-Based Bioremediation Strategies Using Metagenomics

    • Niti B. Jadeja, Atya Kapley
    Pages 195-208

  11. Nanopore Sequencing Techniques: A Comparison of the MinKNOW and the Alignator Sequencers

    • Sebastian Oeck, Alicia I. Tüns, Alexander Schramm
    Pages 209-221

  12. MAIRA: Protein-based Analysis of MinION Reads on a Laptop

    • Caner Bağcı, Benjamin Albrecht, Daniel H. Huson
    Pages 223-234

  13. Recovery and Analysis of Long-Read Metagenome-Assembled Genomes

    • Krithika Arumugam, Irina Bessarab, Mindia A. S. Haryono, Rohan B. H. Williams
    Pages 235-259

  14. Cloud Computing for Metagenomics: Building a Personalized Computational Platform for Pipeline Analyses

    • Martin Callaghan
    Pages 261-279

  15. Artificial Intelligence in Medicine: Microbiome-Based Machine Learning for Phenotypic Classification

    • Xi Cheng, Bina Joe
    Pages 281-288

  16. Tracking Antibiotic Resistance from the Environment to Human Health

    • Eman Abdelrazik, Mohamed El-Hadidi
    Pages 289-301

  17. Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset

    • Pui Yi Maria Yung, Shi Ming Tan
    Pages 303-315

  18. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data

    • Mihnea R. Mangalea, Kristopher Keift, Breck A. Duerkop, Karthik Anantharaman
    Pages 317-337

  19. Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R

    • Alex Coleman, Martin Callaghan
    Pages 339-357

  20. Metagenomics Data Visualization Using R

    • Alex Coleman, Anupam Bose, Suparna Mitra
    Pages 359-392
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Keywords

About this book

This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis usingmost used R packages. 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, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.

 

Editors and Affiliations

  • Leeds Institute of Medical Research, University of Leeds, Leeds, UK

    Suparna Mitra

Bibliographic Information

  • Book Title: Metagenomic Data Analysis

  • Editors: Suparna Mitra

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3072-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3071-6Published: 02 June 2023

  • Softcover ISBN: 978-1-0716-3074-7Due: 11 September 2023

  • eBook ISBN: 978-1-0716-3072-3Published: 31 May 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 441

  • Number of Illustrations: 12 b/w illustrations, 168 illustrations in colour

  • Topics: Genetics and Genomics, Microbial Genetics and Genomics

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