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From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data

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Clostridium difficile

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1476))

Abstract

This chapter presents a method to process C. difficile whole-genome next-generation sequencing data straight from the sequencer. Quality control processing and de novo assembly of these data enable downstream analyses such as gene annotation and in silico multi-locus strain-type identification.

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Author information

Authors and Affiliations

  1. National Institute for Biological Standards and Control, South Mimms, UK

    Mark D. Preston

  2. Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK

    Richard A. Stabler

Authors
  1. Mark D. Preston
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  2. Richard A. Stabler
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Corresponding author

Correspondence to Richard A. Stabler .

Editor information

Editors and Affiliations

  1. Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom

    Adam P. Roberts

  2. Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom

    Peter Mullany

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© 2016 Springer Science+Business Media New York

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Preston, M.D., Stabler, R.A. (2016). From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data. In: Roberts, A., Mullany, P. (eds) Clostridium difficile. Methods in Molecular Biology, vol 1476. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6361-4_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6361-4_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6359-1

  • Online ISBN: 978-1-4939-6361-4

  • eBook Packages: Springer Protocols

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