Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Fast gapped-read alignment with Bowtie 2

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

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

Accession codes

Accessions

Sequence Read Archive

References

  1. McKenna, A. et al. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  Google Scholar 

  2. Trapnell, C. et al. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  Google Scholar 

  3. Langmead, B., Hansen, K.D. & Leek, J.T. Genome Biol. 11, R83 (2010).

    Article  Google Scholar 

  4. Li, H. & Homer, N. Brief. Bioinform. 11, 473–483 (2010).

    Article  CAS  Google Scholar 

  5. Ferragina, P. & Manzini, G. Proc. 41st Annual Symposium on Foundations of Computer Science 390–398 (IEEE Comput. Soc.; 2000).

  6. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  7. Lam, T. et al. IEEE International Conference on Bioinformatics and Biomedicine 31–36 (2009).

  8. Li, H. & Durbin, R. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  9. Li, H. & Durbin, R. Bioinformatics 26, 589–595 (2010).

    Article  Google Scholar 

  10. Li, R. et al. Bioinformatics 25, 1966–1967 (2009).

    Article  CAS  Google Scholar 

  11. Ajay, S.S., Parker, S.C., Ozel Abaan, H., Fuentes Fajardo, K.V. & Margulies, E.H. Genome Res. 21, 1498–1505 (2010).

    Article  Google Scholar 

  12. 1000 Genomes Project Consortium. Nature 467, 1061–1073 (2010).

  13. Rothberg, J.M. et al. Nature 475, 348–352 (2011).

    Article  CAS  Google Scholar 

  14. Li, H. et al. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

Download references

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

Authors

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.

Ethics declarations

Competing interests

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)

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

This article is cited by

Search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research