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Fast gapped-read alignment with Bowtie 2

Nature Methods volume 9, pages 357–359 (2012)Cite this article

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Abstract

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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Figure 1: Alignment comparison using HiSeq 2000, 454 and Ion Torrent reads.
Figure 2: Sensitivity and accuracy of alignment using simulated reads.

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Sequence Read Archive

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Acknowledgements

This work was supported in part by US National Institutes of Health grants R01-HG006102 and R01-GM083873 to S.L.S. and an Amazon Web Services in Education Research grant to B.L. in July 2011.

Author information

Authors and Affiliations

  1. Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA

    Ben Langmead & Steven L Salzberg

  2. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

    Ben Langmead & Steven L Salzberg

  3. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Steven L Salzberg

Authors
  1. Ben Langmead
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  2. Steven L Salzberg
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Contributions

B.L. wrote the software and conducted the experiments. B.L. and S.L.S. wrote the manuscript.

Corresponding author

Correspondence to Ben Langmead.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–2,4–6, Supplementary Note, Supplementary Results (PDF 1017 kb)

Supplementary Table 3

Number of correct and incorrect alignments for sensitivity and accuracy comparisons. (XLS 121 kb)

Supplementary Software

Bowtie 2 source code (ZIP 5453 kb)

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Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923

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