High Throughput Sequencing And Metagenomic Data Analysis
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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.
Bioinformatics For High Throughput Sequencing
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Author : Naiara Rodríguez-Ezpeleta
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-10-26
Bioinformatics For High Throughput Sequencing written by Naiara Rodríguez-Ezpeleta and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-10-26 with Science categories.
Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.
Computational Approaches For Metagenomic Analysis Of High Throughput Sequencing Data
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Author : David Ainsworth
language : en
Publisher:
Release Date : 2016
Computational Approaches For Metagenomic Analysis Of High Throughput Sequencing Data written by David Ainsworth and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
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.
Field Guidelines For Genetic Experimental Designs In High Throughput Sequencing
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Author : Ana M. Aransay
language : en
Publisher: Springer
Release Date : 2016-06-02
Field Guidelines For Genetic Experimental Designs In High Throughput Sequencing written by Ana M. Aransay and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-06-02 with Medical categories.
High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.
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.
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.
Genome Scale Algorithm Design
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Author : Veli Mäkinen
language : en
Publisher: Cambridge University Press
Release Date : 2015-05-07
Genome Scale Algorithm Design written by Veli Mäkinen and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-05-07 with Mathematics categories.
Provides an integrated picture of the latest developments in algorithmic techniques, with numerous worked examples, algorithm visualisations and exercises.
Introduction To Computational Metagenomics
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Author : Zhong Wang
language : en
Publisher: World Scientific
Release Date : 2022-04-11
Introduction To Computational Metagenomics written by Zhong Wang and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-11 with Science categories.
Breakthroughs in high-throughput genome sequencing and high-performance computing technologies have empowered scientists to decode many genomes including our own. Now they have a bigger ambition: to fully understand the vast diversity of microbial communities within us and around us, and to exploit their potential for the improvement of our health and environment. In this new field called metagenomics, microbial genomes are sequenced directly from the habitats without lab cultivation. Computational metagenomics, however, faces both a data challenge that deals with tens of tera-bases of sequences and an algorithmic one that deals with the complexity of thousands of species and their interactions.This interdisciplinary book is essential reading for those who are interested in beginning their own journey in computational metagenomics. It is a prism to look through various intricate computational metagenomics problems and unravel their three distinctive aspects: metagenomics, data engineering, and algorithms. Graduate students and advanced undergraduates from genomics science or computer science fields will find that the concepts explained in this book can serve as stepping stones for more advanced topics, while metagenomics practitioners and researchers from similar disciplines may use it to broaden their knowledge or identify new research targets.