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

Posted by

By Ion Mandoiu, Alexander Zelikovsky

Introduces readers to middle algorithmic suggestions for next-generation sequencing (NGS) information research and discusses a variety of computational suggestions and applications 

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

Part I specializes in computing and experimental infrastructure for NGS research, together with chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling suggestions for large viral sequencing, and high-fidelity sequencing protocols.

Part II concentrates on research of DNA sequencing info, protecting 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 info. This half discusses algorithms and compares software program instruments for transcriptome meeting besides equipment for detection of different splicing and instruments for transcriptome quantification and differential expression analysis. 

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

Computational equipment for subsequent new release Sequencing information Analysis:

  • Reviews computational strategies resembling new combinatorial optimization tools, facts constructions, 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, variation detection from NGS reads, and more

This textual content is a reference for biomedical execs drawn to increasing their wisdom of computational concepts for NGS information research. The ebook is additionally necessary for graduate and post-graduate scholars in bioinformatics.

Show description

Read Online or Download Computational Methods for Next Generation Sequencing Data Analysis PDF

Similar bioinformatics books

Modelling and Optimization of Biotechnological Processes

Mostindustrialbiotechnologicalprocessesareoperatedempirically. Oneofthe significant di? culties of using complicated keep an eye on theories is the hugely nonlinear nature of the strategies. This publication examines methods according to arti? cial intelligencemethods,inparticular,geneticalgorithmsandneuralnetworks,for tracking, modelling and optimization of fed-batch fermentation tactics.

Web Service Mining: Application to Discoveries of Biological Pathways

Internet carrier Mining: program to Discoveries of organic Pathways offers the key concerns and recommendations to mining prone on the net. This ebook focuses in particular on a reference framework for net carrier mining that's encouraged by means of molecular popularity and the drug discovery approach; often called a molecular-based process.

The Dictionary of Genomics, Transcriptomics and Proteomics

Now in its 5th variation and for the 1st time to be had as an digital product with all entries cross-linked. This very winning long-seller has once more been completely up-to-date and drastically improved. It now includes over 13,000 entries, and comprehensively overlaying genomics, transcriptomics, and proteomics.

Understanding Clinical Data Analysis: Learning Statistical Principles from Published Clinical Research

This textbook includes ten chapters, and is a must-read to all clinical and well-being pros, who have already got simple wisdom of the way to research their scientific information, yet nonetheless, ask yourself, after having performed so, why methods have been played the best way they have been. The e-book can also be a must-read to people who are inclined to submerge within the flood of novel statistical methodologies, as communicated in present medical reviews, and medical conferences.

Extra info for Computational Methods for Next Generation Sequencing Data Analysis

Example text

O’Driscoll A, Daugelaite J, Sleator RD. ‘Big data’, Hadoop and cloud computing in genomics. J Biomed Inform 2013;46(5):774–781. 26. Amazon Elastic Compute Cloud (EC2). com/ec2/. 27. Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol 2011;7(8):1002147. 28. Google App Engine. com. Accessed 2016 Mar 19. 29. Windows Azure. com/. Accessed 2016 Mar 19. CLOUD COMPUTING FOR NEXT-GENERATION SEQUENCING DATA ANALYSIS 23 30. Jin C, Buyya R.

RSD-cloud has two primary phases, that is, BLAST and estimation of evolutionary distance. In the first phase, mappers use BLAST to generate hits for all genomes. In the second phase, mappers conduct ortholog computation to estimate orthologs and evolutionary distances for all genomes. 10, two blocks in step 2 illustrate the above two paralleled phases. All results from RSD-cloud directly go into Amazon S3. Experiments showed that it is able to run more than 300,000 RSD-cloud processes within the EC2 to compute the orthologs for all pairs of 55 genomes by using 100 high-capacity computing nodes (38).

Moore GE et al. Cramming More Components Onto Integrated Circuits. New York; McGraw-Hill; 1965. 9. Walter C. Kryder’s law. Sci Am 2005;293(2):32–33. 10. Reynolds C. As we may communicate. ACM SIGCHI Bull 1998;30(3):40–44. 11. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437(7057):376–380. 12. Bennett S. Solexa Ltd. Pharmacogenomics 2004;5(4):433–438.

Download PDF sample

Rated 5.00 of 5 – based on 14 votes