Bioinformatics for High Throughput Sequencing

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Naiara Rodríguez-Ezpeleta, Michael Hackenberg, Ana M. Aransay
Springer Science & Business Media, Oct 26, 2011 - Science - 255 pages
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Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.

 

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Contents

Introduction
1
Overview of Sequencing Technology Platforms
11
Applications of HighThroughput Sequencing
27
Computational Infrastructure and Basic Data Analysis for HighThroughput Sequencing
55
BaseCalling for Bioinformaticians
67
De Novo ShortRead Assembly
85
ShortRead Mapping
107
DNAProtein Interaction Analysis ChIPSeq
127
Generation and Analysis of GenomeWide DNA Methylation Maps
151
Differential Expression for RNA Sequencing RNASeq Data Mapping Summarization Statistical Analysis and Experimental Design
169
MicroRNA Expression Profiling and Discovery
191
Dissecting Splicing Regulatory Network by Integrative Analysis of CLIPSeq Data
209
Analysis of Metagenomics Data
219
HighThroughput Sequencing Data Analysis Software Current State and Future Developments
231
Index
249
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