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.
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B.L. wrote the software and conducted the experiments. B.L. and S.L.S. wrote the manuscript.
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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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DOI: https://doi.org/10.1038/nmeth.1923
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