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Fast gapped-read alignment with Bowtie 2


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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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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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).

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