Download PDF by Ion Mandoiu, Alexander Zelikovsky: Computational Methods for Next Generation Sequencing Data

By Ion Mandoiu, Alexander Zelikovsky

ISBN-10: 1118169484

ISBN-13: 9781118169483

Introduces readers to middle algorithmic strategies for next-generation sequencing (NGS) facts research and discusses quite a lot of computational suggestions and applications 

This publication presents an in-depth survey of a few of the hot advancements in NGS and discusses mathematical and computational demanding situations in a number of program parts of NGS applied sciences. The 18 chapters featured during this ebook were authored through bioinformatics specialists and characterize the newest paintings in prime labs actively contributing to the fast-growing box of NGS. The e-book is split into 4 parts: 

Part I makes a speciality of computing and experimental infrastructure for NGS research, together with chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling techniques for enormous viral sequencing, and high-fidelity sequencing protocols.

Part II concentrates on research of DNA sequencing facts, overlaying the vintage scaffolding challenge, detection of genomic variations, together with insertions and deletions, and research of DNA methylation sequencing data. 

Part III is dedicated to research of RNA-seq facts. This half discusses algorithms and compares software program instruments for transcriptome meeting in addition to tools for detection of different splicing and instruments for transcriptome quantification and differential expression analysis. 

Part IV explores computational instruments for NGS functions in microbiomics, together with a dialogue on blunders correction of NGS reads from viral populations, tools for viral quasispecies reconstruction, and a survey of state of the art tools and destiny traits in microbiome analysis.

Computational tools for subsequent new release Sequencing info Analysis:

  • Reviews computational recommendations resembling new combinatorial optimization equipment, facts buildings, excessive functionality computing, laptop studying, and inference algorithms
  • Discusses the mathematical and computational demanding situations in NGS technologies
  • Covers NGS blunders correction, de novo genome transcriptome meeting, version detection from NGS reads, and more

This textual content is a reference for biomedical execs attracted to increasing their wisdom of computational suggestions for NGS info research. The ebook is usually worthy for graduate and post-graduate scholars in bioinformatics.

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Accessed 2016 Mar 19. 17. Helicos Biosciences Corporation. com/. Accessed 2016 Mar 19. 18. Ion Torrent. com/. Accessed 2016 Mar 19. 19. The 1000 Genomes Project. org/. Accessed 2016 Mar 19. 20. NCBI News. gov/About/news/16feb2011. Accessed 2016 Mar 19. 21. Mediawiki. net/apps/mediawiki/jnomics. Accessed 2016 Mar 19. 22. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18(5):821–829. 23. Buyya R, Yeo CS, Venugopal S, Broberg J, Brandic I.

33. Gunarathne T, Wu T-L, Choi JY, Bae S-H, Qiu J. Cloud computing paradigms for pleasingly parallel biomedical applications. Concurr Comput Pract Exp 2011;23(17): 2338–2354. 34. Redkar T, Guidici T, Meister T. Windows Azure Platform. Volume 1. Berkeley (CA): Apress; 2011. 35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215(3):403–410. 36. Matsunaga A, Tsugawa M, Fortes J. CloudBlast: combining MapReduce and virtualization on distributed resources for bioinformatics applications.

It allows programmers to apply transformations to each data record and to think in a data-centric manner. In the framework of MapReduce programming model, a job includes three continuous phases: Mapping, Sorting & Merging, and Reducing (31). In mapping, the mapper is the primary unit function, and multiple mappers can be created to fetch and process data records without repeat. The outputs from mapper are all in the form of key/value pair. The sorting & merging phase sorts and groups the outputs according to their keys.

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Computational Methods for Next Generation Sequencing Data Analysis by Ion Mandoiu, Alexander Zelikovsky

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