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Short Read Alignment Using SOAP2

  • Protocol
Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1374))

Abstract

Next-generation sequencing (NGS) technologies have rapidly evolved in the last 5 years, leading to the generation of millions of short reads in a single run. Consequently, various sequence alignment algorithms have been developed to compare these reads to an appropriate reference in order to perform important downstream analysis. SOAP2 from the SOAP series is one of the most commonly used alignment programs to handle NGS data, and it efficiently does so using low computer memory usage and fast alignment speed. This chapter describes the protocol used to align short reads to a reference genome using SOAP2, and highlights the significance of using the in-built command-line options to tune the behavior of the algorithm according to the inputs and the desired results.

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Author information

Authors and Affiliations

  1. University of Queensland, Hartley Teakle Building 83, St Lucia, QLD, 4072, Australia

    Bhavna Hurgobin

  2. School of Plant Biology, University of Western Australia, Perth, WA, 6009, Australia

    Bhavna Hurgobin

Authors
  1. Bhavna Hurgobin
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Corresponding author

Correspondence to Bhavna Hurgobin .

Editor information

Editors and Affiliations

  1. School of Plant Biology, University of Western Australia, Perth, Australia

    David Edwards

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Hurgobin, B. (2016). Short Read Alignment Using SOAP2. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_13

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  • DOI: https://doi.org/10.1007/978-1-4939-3167-5_13

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

  • eBook Packages: Springer Protocols

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