Description
Book SynopsisAiming 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.
Table of ContentsCONTRIBUTORS 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. Mândoiu, 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.Mândoiu, and Alexander Zelikovsky
6 Genomic Variants Detection and Genotyping 133
Jorge Duitama
7 Discovering and Genotyping Twilight Zone Deletions 149
Tobias Marschall and Alexander Schönhuth
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 Töpfer 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. Mândoiu, 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
