Brief Communication | Published:

Fast gapped-read alignment with Bowtie 2

Nature Methods volume 9, pages 357359 (2012) | Download Citation

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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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

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. Search for Ben Langmead in:

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Contributions

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

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ben Langmead.

Supplementary information

PDF files

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    Supplementary Text and Figures

    Supplementary Figures 1–4, Supplementary Tables 1–2,4–6, Supplementary Note, Supplementary Results

Excel files

  1. 1.

    Supplementary Table 3

    Number of correct and incorrect alignments for sensitivity and accuracy comparisons.

Zip files

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    Supplementary Software

    Bowtie 2 source code

About this article

Publication history

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DOI

https://doi.org/10.1038/nmeth.1923

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