Sense from sequence reads: methods for alignment and assembly

  • A Corrigendum to this article was published on 01 June 2010

Abstract

The most important first step in understanding next-generation sequencing data is the initial alignment or assembly that determines whether an experiment has succeeded and provides a first glimpse into the results. In parallel with the growth of new sequencing technologies, several algorithms that align or assemble the large data output of today's sequencing machines have been developed. We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools.

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Figure 1: Schematic of a hash table–based alignment strategy.
Figure 2: The Burrows-Wheeler transform for genomic sequence data.
Figure 3: Constructing and visualizing a de Bruijn graph of a DNA sequence.

Change history

  • 06 May 2010

    In the version of this article initially published online, the caption to Figure 3b was mislabeled. It shows a de Bruijn graph of two plasmids partially overlapping in sequence. The error has been corrected online in the HTML and PDF versions of the article.

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Acknowledgements

The authors acknowledge D. Zerbino and support by the Wellcome Trust and the European Molecular Biology Laboratory.

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Correspondence to Paul Flicek.

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Flicek, P., Birney, E. Sense from sequence reads: methods for alignment and assembly. Nat Methods 6, S6–S12 (2009). https://doi.org/10.1038/nmeth.1376

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