Algorithms for Next-Generation Sequencing Data

Part I. Indexing, Compression, and Storage of NGS Data

1. Algorithms for Indexing Highly Similar DNA Sequences
Nadia Ben Nsira, Thierry Lecroq, Mourad Elloumi

2. Full-Text Indexes for High-Throughput Sequencing
David Weese, Enrico Siragusa

3. Searching and Indexing Circular Patterns
Costas S. Iliopoulos, Solon P. Pissis, M. Sohel Rahman

4. De Novo NGS Data Compression
Gaetan Benoit, Claire Lemaitre, Guillaume Rizk, Erwan Drezen, Dominique Lavenier

5. Cloud Storage-Management Techniques for NGS Data
Evangelos Theodoridis

Part II. Error Correction in NGS Data

6. Probabilistic Models for Error Correction of Nonuniform Sequencing Data
Marcel H. Schulz, Ziv Bar-Joseph

7. DNA-Seq Error Correction Based on Substring Indices
David Weese, Marcel H. Schulz, Hugues Richard

8. Error Correction in Methylation Profiling From NGS Bisulfite Protocols
Guillermo Barturen, José L. Oliver, Michael Hackenberg

Part III. Alignment of NGS Data

9. Comparative Assessment of Alignment Algorithms for NGS Data: Features, Considerations, Implementations, and Future
Carol Shen, Tony Shen, Jimmy Lin

10. CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment
Yongchao Liu, Bertil Schmidt

11. String-Matching and Alignment Algorithms for Finding Motifs in NGS Data
Giulia Fiscon, Emanuel Weitschek

Part IV. Assembly of NGS Data

12. The Contig Assembly Problem and Its Algorithmic Solutions
Géraldine Jean, Andreea Radulescu, Irena Rusu

13. An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties
Tomáš Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis

14. Assembly-Free Techniques for NGS Data
Matteo Comin, Michele Schimd

Keywords: Computer Science, Computational Biology/Bioinformatics, Mathematical and Computational Biology, Bioinformatics, Algorithm Analysis and Problem Complexity