Metagenomic Data Analysis
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Metagenomic Data Analysis
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Author : Suparna Mitra
language : en
Publisher: Springer Nature
Release Date : 2023-05-31
Metagenomic Data Analysis written by Suparna Mitra and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-31 with Science categories.
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.
Metagenomics
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Author : Wael N. Hozzein
language : en
Publisher:
Release Date : 2020
Metagenomics written by Wael N. Hozzein and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with categories.
This book is for the students starting their research projects in the field of metagenomics, for researchers interested in the new developments and applications in this field; and for teachers involved in teaching this subject. The book is divided into three sections as indicated from its title, namely; the basics of metagenomics, metagenomic analysis, and applications of metagenomics. It covers the basics of metagenomics from its history and background, to the analysis of metagenomic data as well as its recent applications in different fields. The book contains excellent texts at both the introductory and advanced levels, that describe the latest metagenomic approaches and applications, from sampling to data analysis for taxonomic, environmental, and medical studies. Finally, the publication of this book was an interesting journey for me and I hope the readers will enjoy reading it.
Metagenomics For Microbiology
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Author : Jacques Izard
language : en
Publisher: Academic Press
Release Date : 2014-11-07
Metagenomics For Microbiology written by Jacques Izard and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-11-07 with Science categories.
Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.
Metagenomics
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Author : Wael N. Hozzein
language : en
Publisher: BoD – Books on Demand
Release Date : 2020-03-25
Metagenomics written by Wael N. Hozzein and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-25 with Science categories.
This book is for the students starting their research projects in the field of metagenomics, for researchers interested in the new developments and applications in this field; and for teachers involved in teaching this subject. The book is divided into three sections as indicated from its title, namely; the basics of metagenomics, metagenomic analysis, and applications of metagenomics. It covers the basics of metagenomics from its history and background, to the analysis of metagenomic data as well as its recent applications in different fields. The book contains excellent texts at both the introductory and advanced levels, that describe the latest metagenomic approaches and applications, from sampling to data analysis for taxonomic, environmental, and medical studies. Finally, the publication of this book was an interesting journey for me and I hope the readers will enjoy reading it.
Statistical Analysis Of Microbiome Data With R
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Author : Yinglin Xia
language : en
Publisher: Springer
Release Date : 2018-10-06
Statistical Analysis Of Microbiome Data With R written by Yinglin Xia and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-10-06 with Computers categories.
This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.
Statistical Analysis Of Microbiome Data
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Author : Somnath Datta
language : en
Publisher: Springer Nature
Release Date : 2021-10-27
Statistical Analysis Of Microbiome Data written by Somnath Datta and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-27 with Medical categories.
Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.
Metagenomic Data Analysis
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Author : Fabio Gori
language : en
Publisher:
Release Date : 2013
Metagenomic Data Analysis written by Fabio Gori and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
High Throughput Sequencing And Metagenomic Data Analysis
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Author : Ahmed M. Mohammed Shuikan
language : en
Publisher:
Release Date : 2019
High Throughput Sequencing And Metagenomic Data Analysis written by Ahmed M. Mohammed Shuikan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with Science categories.
Metagenomic approaches are a growing branch of science and have many applications in different fields. Metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soils and to study how this biodiversity is affected with continuously changing conditions. In addition, its application in clinical and diagnostic approaches was reported. The emergence of several next-generation sequencing (NGS) strategies enriched the metagenomics. The combination between NGS and metagenomic approaches helped the investigators resolve several issues regarding the microbial diversity and the functions and relationships among different microbial flora. A number of NGS approaches were developed including Roche/454 pyrosequencing, Illumina/Solexa sequencing, and Applied Biosystems/SOLiD sequencing. In this chapter, different NGS platforms are discussed in terms of principle, advantages, and limitations. In addition, third-generation sequencing technologies are also addressed.
Statistical Analysis Of Metagenomic Data
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Author : Viktor Jonsson
language : en
Publisher:
Release Date : 2014
Statistical Analysis Of Metagenomic Data written by Viktor Jonsson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
The New Science Of Metagenomics
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Author : National Research Council
language : en
Publisher: National Academies Press
Release Date : 2007-06-24
The New Science Of Metagenomics written by National Research Council and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-06-24 with Science categories.
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.