Editors:
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)
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Front Matter
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 using most 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.
Keywords
- Sequencing
- microbial ecosystem
- MinION sequencing
- Next-Generation Sequencing
- shotgun metagenomics
Editors and Affiliations
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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: 16 June 2024
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