- Brief Communication
- Published:
Fast gapped-read alignment with Bowtie 2
Nature Methodsvolume 9, pages357–359 (2012)Cite this article
105kAccesses
169Altmetric
Subjects
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
Subscription info for Japanese customers
We have a dedicated website for our Japanese customers. Please go tonatureasia.com to subscribe to this journal.
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
McKenna, A. et al.Genome Res.20, 1297–1303 (2010).
Trapnell, C. et al.Nat. Biotechnol.28, 511–515 (2010).
Langmead, B., Hansen, K.D. & Leek, J.T.Genome Biol.11, R83 (2010).
Li, H. & Homer, N.Brief. Bioinform.11, 473–483 (2010).
Ferragina, P. & Manzini, G.Proc. 41st Annual Symposium on Foundations of Computer Science 390–398 (IEEE Comput. Soc.; 2000).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L.Genome Biol.10, R25 (2009).
Lam, T. et al. IEEE International Conference on Bioinformatics and Biomedicine 31–36 (2009).
Li, H. & Durbin, R.Bioinformatics25, 1754–1760 (2009).
Li, H. & Durbin, R.Bioinformatics26, 589–595 (2010).
Li, R. et al.Bioinformatics25, 1966–1967 (2009).
Ajay, S.S., Parker, S.C., Ozel Abaan, H., Fuentes Fajardo, K.V. & Margulies, E.H.Genome Res.21, 1498–1505 (2010).
1000 Genomes Project Consortium.Nature467, 1061–1073 (2010).
Rothberg, J.M. et al.Nature475, 348–352 (2011).
Li, H. et al.Bioinformatics25, 2078–2079 (2009).
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
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
Ben Langmead & Steven L Salzberg
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
Ben Langmead & Steven L Salzberg
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Steven L Salzberg
- Ben Langmead
You can also search for this author inPubMed Google Scholar
- Steven L Salzberg
You can also search for this author inPubMed Google Scholar
Contributions
B.L. wrote the software and conducted the experiments. B.L. and S.L.S. wrote the manuscript.
Corresponding author
Correspondence toBen 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
About this article
Cite this article
Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2.Nat Methods9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923
Received:
Accepted:
Published:
Issue Date:
Share this article
Anyone you share the following link with will be able to read this content:
Sorry, a shareable link is not currently available for this article.
Provided by the Springer Nature SharedIt content-sharing initiative
