Computational methods for next generation sequencing data analysis
Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational ch...
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| Hlavní autoři: | , |
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| Médium: | E-kniha Kniha |
| Jazyk: | angličtina |
| Vydáno: |
Hoboken, N.J
Wiley
2016
John Wiley & Sons, Incorporated Wiley-Blackwell |
| Vydání: | 1 |
| Edice: | Wiley series in bioinformatics |
| Témata: | |
| ISBN: | 1118169484, 9781118169483, 1119272173, 9781119272175 |
| On-line přístup: | Získat plný text |
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- Cover -- Title Page -- Copyright -- Contents -- Contributors -- Preface -- About the Companion Website -- Part I Computing and Experimental Infrastructure for NGS -- Chapter 1 Cloud Computing for Next-Generation Sequencing Data Analysis -- 1.1 Introduction -- 1.2 Challenges for NGS Data Analysis -- 1.3 Background For Cloud Computing and its Programming Models -- 1.4 Cloud Computing Services for NGS Data Analysis -- 1.5 Conclusions and Future Directions -- References -- Chapter 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways -- 2.1 Introduction & -- Overview -- 2.2 Background -- 2.3 Metapathways Processes -- 2.4 Big Data Processing -- 2.5 Downstream Analyses -- 2.6 Conclusions -- References -- Chapter 3 Pooling Strategy for Massive Viral Sequencing -- 3.1 Introduction -- 3.2 Design of Pools for Big Viral Data -- 3.3 Deconvolution of Viral Samples From Pools -- 3.4 Performance of Pooling Methods on Simulated Data -- 3.5 Experimental Validation of Pooling Strategy -- 3.6 Conclusion -- References -- Chapter 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses -- 4.1 Introduction -- 4.2 High-Fidelity Sequencing Protocol -- 4.3 Assembly of High-Fidelity Sequencing Data -- 4.4 Performance of VGA on Simulated Data -- 4.5 Performance of Existing Viral Assemblers on Simulated Consensus Error-Corrected Reads -- 4.6 Performance of VGA on Real Hiv Data -- 4.7 Comparison of Alignment on Error-Corrected Reads -- 4.8 Evaluating of Error Correction Tools Based on High-Fidelity Sequencing Reads -- Acknowledgment -- References -- Part II Genomics and Epigenomics -- Chapter 5 Scaffolding Algorithms -- 5.1 Scaffolding -- 5.2 State-of-The-Art Scaffolding Tools -- 5.3 Recent Scaffolding Tools -- 5.4 Scaffolding Software Evaluation -- References -- Chapter 6 Genomic Variants Detection and Genotyping
- 12.5 Comparison -- 12.6 Results -- 12.7 Summary and Conclusion -- Acknowledgments -- References -- Chapter 13 Computational Approaches for Studying Alternative Splicing in Nonmodel Organisms From RNA-SEQ Data -- 13.1 Introduction -- 13.2 Representation of Alternative Splicing -- 13.3 Comparison to Model Organisms -- 13.4 Accuracy of Algorithms -- 13.5 Discussion -- References -- Chapter 14 Transcriptome Quantification and Differential Expression From NGS Data -- 14.1 Introduction -- 14.2 Overview of the State-of-the-Art Methods -- 14.3 Recent Algorithms -- 14.4 Experimental Setup -- 14.5 Evaluation -- AcknowledgmentS -- References -- Part IV Microbiomics -- Chapter 15 Error Correction of NGS Reads from Viral Populations -- 15.1 Next-Generation Sequencing of Heterogeneous Viral Populations and Sequencing Errors -- 15.2 Methods and Algorithms for The Ngs Error Correction in Viral Data -- 15.3 Algorithm Comparison -- References -- Chapter 16 Probabilistic Viral Quasispecies Assembly -- 16.1 Intra-Host Virus Populations -- 16.2 Next-Generation Sequencing for Viral Genomics -- 16.3 Probabilistic Reconstruction Methods -- 16.4 Conclusion -- References -- Chapter 17 Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data -- 17.1 Introduction -- 17.2 Background -- 17.3 Methods -- 17.4 Results and Discussion -- Acknowledgments -- References -- Chapter 18 Microbiome Analysis: State of the Art and Future Trends -- 18.1 Introduction -- 18.2 The Metagenomics Analysis Pipeline -- 18.3 Data Limitations and Sources of Errors -- 18.4 Diversity and Richness Measures -- 18.5 Correlations and Association Rules -- 18.6 Microbial Functional Profiles -- 18.7 Microbial Social Interactions and Visualizations -- 18.8 Bayesian Inferences -- 18.9 Conclusion -- References -- Index -- EULA
- 6.1 Introduction -- 6.2 Methods for Detection and Genotyping OF SNPs and Small Indels -- 6.3 Methods for Detection and Genotyping of CNVs -- 6.4 Putting Everything Together -- References -- Chapter 7 Discovering and Genotyping Twilight Zone Deletions -- 7.1 Introduction -- 7.2 Notation -- 7.3 Non-Twilight-Zone Deletion Discovery -- 7.4 Discovering "Twilight Zone" Deletions: New Solutions -- 7.5 Genotyping "Twilight Zone" Deletions -- 7.6 Results -- 7.7 Discussion -- 7.8 Availability -- Acknowledgments -- References -- Chapter 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data -- 8.1 Background -- 8.2 Methods -- 8.3 Applications -- 8.4 Conclusions and Future Directions -- Acknowledgment -- References -- Chapter 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies -- 9.1 Introduction -- 9.2 Enrichment-Based Approaches -- 9.3 Bisulfite Treatment-Based Approaches -- 9.4 Conclusion -- References -- Chapter 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis -- 10.1 Introduction -- 10.2 The Problem of Mapping BS-Treated Reads -- 10.3 Algorithmic Approaches to the Problem Of Mapping BS-Treated Reads -- 10.4 Methylation Estimation -- 10.5 Possible Biases in Estimation of Methylation Level -- 10.6 Bisulfite Conversion Rate -- 10.7 Reduced Representation Bisulfite Sequencing -- 10.8 Accuracy as a Performance Measurement -- References -- Part III Transcriptomics -- Chapter 11 Computational Methods for Transcript Assembly from RNA-SEQ Reads -- 11.1 Introduction -- 11.2 De Novo Assembly -- 11.3 Genome-Based Assembly -- 11.4 Conclusions -- Acknowledgment -- References -- Chapter 12 An Overview And Comparison of Tools for RNA-Seq Assembly -- 12.1 Quality Assessment -- 12.2 Experimental Considerations -- 12.3 Assembly -- 12.4 Experiment