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

Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Whole-genome sequencing Sequencing High-throughput sequencing Illumina HiSeq X HTS NGS Quality control Preprocessing Alignment Mapping 

Notes

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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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Marvin N. Wright
    • 1
  • Damian Gola
    • 1
  • Andreas Ziegler
    • 1
  1. 1.Institut für Medizinische Biometrie und StatistikUniversität zu Lübeck, Universitätsklinikum Schleswig-Holstein - Campus LübeckLübeckGermany

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