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Next-Generation Sequencing Technologies and Fragment Assembly Algorithms

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Evolutionary Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 855))

Abstract

As a classic topic in bioinformatics, the fragment assembly problem has been studied for over two decades. Fragment assembly algorithms take a set of DNA fragments as input, piece them together into a set of aligned overlapping fragments (i.e., contigs), and output a consensus sequence for each of the contigs. The rapid advance of massively parallel sequencing, often referred to as next-generation sequencing (NGS) technologies, has revolutionized DNA sequencing by reducing both its time and cost by several orders of magnitude in the past few years, but posed new challenges for fragment assembly. As a result, many new approaches have been developed to assemble NGS sequences, which are typically shorter with a higher error rate, but at a much higher throughput, than classic methods provided. In this chapter, we review both classic and new algorithms for fragment assembly, with a focus on NGS sequences. We also discuss a few new assembly problems emerging from the broader applications of NGS techniques, which are distinct from the classic fragment assembly problem.

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Authors and Affiliations

  1. School of Informatics and Computing, Indiana University, Bloomington, IN, USA

    Heewook Lee & Haixu Tang

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  1. Heewook Lee
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  2. Haixu Tang
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Correspondence to Haixu Tang .

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Editors and Affiliations

  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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Lee, H., Tang, H. (2012). Next-Generation Sequencing Technologies and Fragment Assembly Algorithms. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 855. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-582-4_5

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  • DOI: https://doi.org/10.1007/978-1-61779-582-4_5

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-581-7

  • Online ISBN: 978-1-61779-582-4

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