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Variant Calling
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Download or read book Variant Calling written by Charlotte Ng and published by Springer Nature. This book was released on 2022-06-25 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
Book Synopsis Genomics in the Cloud by : Geraldine A. Van der Auwera
Download or read book Genomics in the Cloud written by Geraldine A. Van der Auwera and published by O'Reilly Media. This book was released on 2020-04-02 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra
Book Synopsis Algorithms for Next-Generation Sequencing Data by : Mourad Elloumi
Download or read book Algorithms for Next-Generation Sequencing Data written by Mourad Elloumi and published by Springer. This book was released on 2017-09-18 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignment; and assembly. The book will be of value to researchers, practitioners and students engaged with bioinformatics, computer science, mathematics, statistics and life sciences.
Book Synopsis Molecular Plant Breeding by : Yunbi Xu
Download or read book Molecular Plant Breeding written by Yunbi Xu and published by CABI. This book was released on 2010 with total page 756 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in plant genomics and molecular biology have revolutionized our understanding of plant genetics, providing new opportunities for more efficient and controllable plant breeding. Successful techniques require a solid understanding of the underlying molecular biology as well as experience in applied plant breeding. Bridging the gap between developments in biotechnology and its applications in plant improvement, Molecular Plant Breeding provides an integrative overview of issues from basic theories to their applications to crop improvement including molecular marker technology, gene mapping, genetic transformation, quantitative genetics, and breeding methodology.
Book Synopsis Computational Exome and Genome Analysis by : Peter N. Robinson
Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
Book Synopsis The Spruce Genome by : Ilga M. Porth
Download or read book The Spruce Genome written by Ilga M. Porth and published by Springer. This book was released on 2021-08-16 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers comprehensive information on the genomics of spruces (Picea spp.), naturally abundant conifer tree species that are widely distributed in the Northern Hemisphere. Due to their tremendous ecological and economic importance, the management of forest genetic resources has chiefly focused on conservation and tree improvement. A draft genome sequence of the 20-gigabase Norway spruce genome was published in the journal Nature in 2013. Continuous efforts to improve the spruce genome assembly are underway, but are hindered by the inherent characteristics of conifer genomes: high amounts of repetitive sequences (introns and transposable elements) in the genome and large gene family expansions with regards to abiotic stress, secondary metabolism and spruces' defense responses to pathogens and herbivory. This book presents the latest information on the status of genome assemblies, provides detailed insights into transposable elements and methylation patterns, and highlights the extensive genomic resources available for inferring population genomics and climate adaptation, as well as emerging genomics tools for tree improvement programs. In addition, this volume features whole-genome comparisons among conifer species, and demonstrates how functional genomics can be used to improve gene function annotations. The book closes with an outlook on emerging fields of research in spruce genomics.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
Book Synopsis Genome-Scale Algorithm Design by : Veli Mäkinen
Download or read book Genome-Scale Algorithm Design written by Veli Mäkinen and published by Cambridge University Press. This book was released on 2023-10-12 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.
Download or read book Variant written by Robison Wells and published by Harper Collins. This book was released on 2011-10-04 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Benson Fisher thought that a scholarship to Maxfield Academy would be the ticket out of his dead-end life. He was wrong. Now he’s trapped in a school that’s surrounded by a razor-wire fence. A school where video cameras monitor his every move. Where there are no adults. Where the kids have split into groups in order to survive. Where breaking the rules equals death. But when Benson stumbles upon the school’s real secret, he realizes that playing by the rules could spell a fate worse than death, and that escape—his only real hope for survival—may be impossible.
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309453291 Total Pages :149 pages Book Rating :4.3/5 (94 download)
Book Synopsis An Evidence Framework for Genetic Testing by : National Academies of Sciences, Engineering, and Medicine
Download or read book An Evidence Framework for Genetic Testing written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-04-21 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in genetics and genomics are transforming medical practice, resulting in a dramatic growth of genetic testing in the health care system. The rapid development of new technologies, however, has also brought challenges, including the need for rigorous evaluation of the validity and utility of genetic tests, questions regarding the best ways to incorporate them into medical practice, and how to weigh their cost against potential short- and long-term benefits. As the availability of genetic tests increases so do concerns about the achievement of meaningful improvements in clinical outcomes, costs of testing, and the potential for accentuating medical care inequality. Given the rapid pace in the development of genetic tests and new testing technologies, An Evidence Framework for Genetic Testing seeks to advance the development of an adequate evidence base for genetic tests to improve patient care and treatment. Additionally, this report recommends a framework for decision-making regarding the use of genetic tests in clinical care.
Book Synopsis Computational Genomics with R by : Altuna Akalin
Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Book Synopsis Virus Bioinformatics by : Manja Marz
Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.
Author :International Commission on Zoological Nomenclature Publisher :Univ of California Press ISBN 13 :9780853010036 Total Pages :364 pages Book Rating :4.0/5 (1 download)
Book Synopsis Code International de Nomenclature Zoologique by : International Commission on Zoological Nomenclature
Download or read book Code International de Nomenclature Zoologique written by International Commission on Zoological Nomenclature and published by Univ of California Press. This book was released on 1985 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Delphi in a Nutshell by : Ray Lischner
Download or read book Delphi in a Nutshell written by Ray Lischner and published by "O'Reilly Media, Inc.". This book was released on 2000-03-16 with total page 579 pages. Available in PDF, EPUB and Kindle. Book excerpt: The opening chapters discuss the Delphi object model, runtime type information and concurrent programming, while the bulk of the book is a language reference with every keyword, directive, function, procedure, variable, class, method, and property that is part of Delphi Pascal. Annotation copyrighted by Book News, Inc., Portland, OR
Book Synopsis Single Nucleotide Polymorphisms by : Pui-Yan Kwok
Download or read book Single Nucleotide Polymorphisms written by Pui-Yan Kwok and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive collection of readily reproducible techniques for the difficult process of single nucleotide polymorphisms (SNP) discovery and genotyping. These cutting-edge protocols for mutation/SNP detection utilize denaturing high-performance liquid chromatography (dHPLC), single-strand conformation polymorphism (SSCP), conformation-sensitive gel electrophoresis (CSGE), chemical cleavage, and direct sequencing. Equally powerful and up-to-date methods are given for genotyping SNPs, including molecular beacons, the Taqman assay, single-base extension approaches, pyrosequencing, ligation, the Invader assay, and primer extension with mass spectrometry detection.
Book Synopsis Classroom Instruction that Works by : Robert J. Marzano
Download or read book Classroom Instruction that Works written by Robert J. Marzano and published by ASCD. This book was released on 2001 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: Describes nine different teaching strategies which have been proven to have positive effects on student learning and explains how those strategies can be incorporated into the classroom.
Book Synopsis Current Protocols in Bioinformatics by : Andreas D. Baxevanis
Download or read book Current Protocols in Bioinformatics written by Andreas D. Baxevanis and published by Current Protocols. This book was released on 2003 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Protocols in Bioinformatics is the only publication that responds to the need for both a current and updateable source of bioinformatics methodology. This unique publication assures that you have access to a full range of bioinformatics protocols written by globally-recognized experts in the field, and that these proto-cols are updated and revised as new developments and innovations occur.
