Identification of Nucleotide Variation in Genomes Using Next-Generation Sequencing

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Discovery of genome-wide variation has taken a huge leap forward with the introduction of next-generation sequencing (NGS) technology. Variant discovery requires sampling of a number of haplotypes. This can be either the two haplotypes of a diploid organism or multiple haplotypes in a population. Variant discovery can be done by sequencing pooled DNA and NGS makes it cost-effective to sample many haplotypes. In this chapter, we discuss various sequencing strategies for variation discovery, focusing mainly on single nucleotide polymorphisms, and to a lesser extent on short insertion/deletions (Indels). We discuss different options, such as specific library construction and the amount of sequencing required to meet a certain objective. While the benefits of NGS to their own research may be obvious to many researchers, the main obstacle for applying NGS is often practical - how to manipulate and analyze the amount of data from a typical NGS run. The methods therefore focus on practical considerations dealing with large NGS datasets, such as sequence processing and filtering, mapping to a reference genome, and variant calling. In addition, we focus on data standards and tools to manipulate and analyze data from such standardized datasets. By providing examples and links to easy-to-implement scripts and software, we hope to lower the threshold for biologists to further explore the wealth of information that can be obtained by these new molecular resources
Original languageEnglish
Title of host publicationTag-Based Next Generation Sequencing
EditorsM. Harbers, G. Kahl
Place of PublicationWeinheim, Germany
PublisherWiley-VCH
Pages257-276
Number of pages581
ISBN (Print)9783527328192
DOIs
Publication statusPublished - 2012

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