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Base-Calling for Bioinformaticians

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Bioinformatics for High Throughput Sequencing

Abstract

High-throughput platforms execute billions of simultaneous sequencing reactions. Base-calling is the process of decoding the output signals of these reactions into sequence reads. In this chapter, we detail the facets of base-calling using the perspective of signal communication. We primarily focus on the Illumina high-throughput sequencing platform and review different third-party base-calling implementations.

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Acknowledgments

The authors would like to thank Fabian Menges, Giuseppe Narzisi, and Bud Mishra for sharing their early TotalReCaller results, for Dan Valente for formulating the unified distortion model, and for Dina Esposito for useful comments on the chapter. Yaniv Erlich is an Andria and Paul Heafy family fellow.

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Authors and Affiliations

  1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA

    Mona A. Sheikh & Yaniv Erlich

Authors
  1. Mona A. Sheikh
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  2. Yaniv Erlich
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Corresponding author

Correspondence to Yaniv Erlich .

Editor information

Editors and Affiliations

  1. CIC bioGUNE, Genome Analysis Platform, Derio, 48160, Spain

    Naiara Rodríguez-Ezpeleta

  2. Computational Genomics and Bioinformatic, University of Granada, Genetics Department & Biomedical Research Center (CIBM), Granada, Spain

    Michael Hackenberg

  3. CIC bioGUNE, Genome Analysis Platform, Derio, 48160, Spain

    Ana M. Aransay

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Sheikh, M.A., Erlich, Y. (2012). Base-Calling for Bioinformaticians. In: Rodríguez-Ezpeleta, N., Hackenberg, M., Aransay, A. (eds) Bioinformatics for High Throughput Sequencing. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0782-9_5

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