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Genome Assembly

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Fungal Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1775))

Abstract

Genome assembly uses sequence similarity to go from sequencing reads to longer contiguous sequences (contigs). Scaffolds are contigs linked together by gaps where the order and orientation of the contigs is known but the exact sequence connecting two contigs is unknown, represented by Ns which estimate the gap length. Here we describe recommendations for genome assembly for different sequencing technologies, describe organelle assembly, and review how to perform assembly quality control.

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Acknowledgment

The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.

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Authors and Affiliations

  1. United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

    Alicia Clum

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  1. Alicia Clum
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Correspondence to Alicia Clum .

Editor information

Editors and Affiliations

  1. Fungal Physiology, Westerdijk Fungal, Biodiversity Institute, Utrecht, The Netherlands

    Ronald P. de Vries

  2. Centre for Structural and Functional Genomics, Concordia University, Montreal, Québec, Canada

    Adrian Tsang

  3. US Department of Energy, Joint Genome Institute, Walnut Creek, California, USA

    Igor V. Grigoriev

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Clum, A. (2018). Genome Assembly. In: de Vries, R., Tsang, A., Grigoriev, I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7804-5_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7804-5_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7803-8

  • Online ISBN: 978-1-4939-7804-5

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