Preface.- Introduction.- Overview of Sequencing Technology Platforms.- Applications of High Throughput Sequencing.- Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing.- Base-Calling for Bioinformaticians.- De Novo Short Read Assembly.- Short Read Mapping.- DNA-Protein Interaction Analysis (ChIP-Seq).- Genome-wide Methylation Maps.- Differential Expression for RNA Sequencing (RNA-seq) Data: Mapping, Summarization, Statistical Analysis and Experimental Design.- MicroRNA Expression Profiling and Discovery.- Dissecting Splicing-Regulatory Network by Integrative Analysis of HITS-CLIP data.- Analysis of Metagenomics Data.- High Throughput Sequencing Data Analysis Software: Current State and Future Developments.- Index.
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.