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Computational Methods for Next Generation Sequencing Data Analysis
Aiming to foster future collaborations between researchers in algorithms, bioinformatics, and molecular biology, this book serves as an up-to-date survey of the most important recent developments and computational challenges in various application areas of next-generation sequencing technologies.
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| Format: | Printed Book |
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Hoboken, New Jersey
Wiley
2016
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| Series: | Wiley series on bioinformatics.
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Table of Contents:
- CONTRIBUTORS xix PREFACE xxiii ABOUT THE COMPANION WEBSITE xxv PART I COMPUTING AND EXPERIMENTAL INFRASTRUCTURE FOR NGS 1 1 Cloud Computing for Next-Generation Sequencing Data Analysis 3 Xuan Guo, Ning Yu, Bing Li, and Yi Pan 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways 25 Niels W. Hanson, Kishori M. Konwar, Shang-Ju Wu, and Steven J. Hallam 3 Pooling Strategy for Massive Viral Sequencing 57 Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, David S. Campo, Zoya Dimitrova, Ion I. Mandoiu, Alexander Zelikovsky, and Yury Khudyakov 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses 85 Serghei Mangul, Nicholas C. Wu, Ekaterina Nenastyeva, Nicholas Mancuso, Alexander Zelikovsky, Ren Sun, and Eleazar Eskin PART II GENOMICS AND EPIGENOMICS 105 5 Scaffolding Algorithms 107 Igor Mandric, James Lindsay, Ion I.Mandoiu, and Alexander Zelikovsky 6 Genomic Variants Detection and Genotyping 133 Jorge Duitama 7 Discovering and Genotyping Twilight Zone Deletions 149 Tobias Marschall and Alexander Schonhuth 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data 175 Jin Zhang, Chong Chu, and Yufeng Wu 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies 197 Jeong-Hyeon Choi and Huidong Shi 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis 227 Elena Harris and Stefano Lonardi PART III TRANSCRIPTOMICS 245 11 Computational Methods for Transcript Assembly from RNA-SEQ Reads 247 Stefan Canzar and Liliana Florea 12 An Overview And Comparison of Tools for RNA-Seq Assembly 269 Rasiah Loganantharaj and Thomas A. Randall 13 Computational Approaches for Studying Alternative Splicing in Nonmodel Organisms From RNA-SEQ Data 287 Sing-Hoi Sze 14 Transcriptome Quantification and Differential Expression From NGS Data 301 Olga Glebova, Yvette Temate-Tiagueu, Adrian Caciula, Sahar Al Seesi, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. M andoiu, and Alexander Zelikovsky PART IV MICROBIOMICS 329 15 Error Correction of NGS Reads from Viral Populations 331 Pavel Skums, Alexander Artyomenko, Olga Glebova, David S. Campo, Zoya Dimitrova, Alexander Zelikovsky, and Yury Khudyakov 16 Probabilistic Viral Quasispecies Assembly 355 Armin Topfer and Niko Beerenwinkel 17 Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data 383 Bassam Tork, Ekaterina Nenastyeva, Alexander Artyomenko, Nicholas Mancuso, Mazhar I. Khan, Rachel O Neill, Ion I. Mandoiu, and Alexander Zelikovsky 18 Microbiome Analysis: State of the Art and Future Trends 401 Mitch Fernandez, Vanessa Aguiar-Pulido, Juan Riveros, Wenrui Huang, Jonathan Segal, Erliang Zeng, Michael Campos, Kalai Mathee, and Giri Narasimhan INDEX 425