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Alignment

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Next Generation Sequencing and Data Analysis

Part of the book series: Learning Materials in Biosciences ((LMB))

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What you will learn

The purposes of the alignment process are to measure distances/similarities between strings and thus to locate origins of Next Generation Sequencing (NGS) reads in a reference genome. Alignment algorithms like BLAST that can be used to search for the location of a single or a small number of sequences in a certain genome are not suitable to align millions of NGS reads. This led to the development of advanced algorithms that can meet this task, allow distinguishing polymorphisms from mutations and sequencing errors from true sequence deviations. For a basic understanding, the differences between global and local alignment and the underlying algorithms are described in a simplified way in this chapter, as well as the main difference between BLAST and NGS alignment is described in a simplified way in this chapter. Moreover, different alignment tools and their basic usage are presented, which enables the reader to perform and understand alignment processes of sequencing reads to any genome using the respective commands.

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Acknowledgements

We are grateful to Dr. Richa Bharti (Bioinformatician at TUM Campus Straubing, Germany) and Dr. Philipp Torkler (Senior Bioinformatics Scientist, Exosome Diagnostics, a Bio-Techne brand, Munich, Germany) for critically reading this text. We thank for correcting our mistakes and suggesting relevant improvements to the original manuscript.

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Authors and Affiliations

  1. Deggendorf Institute of Technology, Deggendorf, Germany

    Melanie Kappelmann-Fenzl

  2. Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany

    Melanie Kappelmann-Fenzl

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  1. Melanie Kappelmann-Fenzl
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Correspondence to Melanie Kappelmann-Fenzl .

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Editors and Affiliations

  1. Faculty of Applied Informatics, Deggendorf Institute of Technology, Deggendorf, Germany

    Melanie Kappelmann-Fenzl

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Kappelmann-Fenzl, M. (2021). Alignment. In: Kappelmann-Fenzl, M. (eds) Next Generation Sequencing and Data Analysis. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-030-62490-3_9

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