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Preprocessing and Quality Control for Whole-Genome Sequences from the Illumina HiSeq X Platform

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Statistical Human Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1666))

Abstract

The advancement of high-throughput sequencing technologies enables sequencing of human genomes at steadily decreasing costs and increasing quality. Before variants can be analyzed, e.g., in association studies, the raw data obtained from the sequencer need to be preprocessed. These preprocessing steps include the removal of adapters, duplicates, and contaminations, alignment to a reference genome and the postprocessing of the alignment. All later steps, such as variant discovery, rely on high data quality and proper preprocessing, emphasizing the great importance of quality control. This chapter presents a workflow for preprocessing Illumina HiSeq X sequencing data. Code snippets are provided for illustrating all necessary steps, along with a brief description of the tools and underlying methods.

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Acknowledgments

The work presented in this chapter was supported by the German Centre for Cardiovascular Research (DZHK; Deutsches Zentrum für Herz-Kreislauf-Forschung) and the DZHK OMICs Resource Project (grant: 81X1700104).

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Author notes

  1. Marvin N. Wright and Damian Gola contributed equally to this work.

Authors and Affiliations

  1. Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein - Campus Lübeck, Lübeck, Germany

    Marvin N. Wright, Damian Gola & Andreas Ziegler

Authors
  1. Marvin N. Wright
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  2. Damian Gola
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  3. Andreas Ziegler
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Corresponding author

Correspondence to Marvin N. Wright .

Editor information

Editors and Affiliations

  1. Case Western Reserve University, Cleveland, OH, USA

    Robert C. Elston

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Wright, M.N., Gola, D., Ziegler, A. (2017). Preprocessing and Quality Control for Whole-Genome Sequences from the Illumina HiSeq X Platform. In: Elston, R. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 1666. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7274-6_30

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  • DOI: https://doi.org/10.1007/978-1-4939-7274-6_30

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7273-9

  • Online ISBN: 978-1-4939-7274-6

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