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Fast and sensitive protein alignment using DIAMOND

Nature Methods volume 12, pages 59–60 (2015)Cite this article

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Abstract

The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.

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Figure 1: Comparison of DIAMOND and RAPSearch2 against BLASTX for four sequencing technologies and for ORFs predicted from a bacterial assembly.

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Sequence Read Archive

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Acknowledgements

This research was partially supported by the National Research Foundation and Ministry of Education Singapore under its Research Centre of Excellence Programme, and by the A*STAR Computational Resource Centre through the use of its high-performance computing facilities.

Author information

Authors and Affiliations

  1. Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany

    Benjamin Buchfink & Daniel H Huson

  2. Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore

    Chao Xie & Daniel H Huson

  3. Life Sciences Institute, National University of Singapore, Singapore

    Chao Xie

Authors
  1. Benjamin Buchfink
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  2. Chao Xie
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  3. Daniel H Huson
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Contributions

B.B. designed and implemented the algorithm. C.X. performed the experimental study. C.X. and D.H.H. initiated and guided the project. D.H.H. and B.B. wrote the manuscript.

Corresponding authors

Correspondence to Benjamin Buchfink or Daniel H Huson.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Spaced seeds.

(a) The four seed shapes of weight 12 that DIAMOND uses by default. Ones and zeros indicate positions to use and ignore, respectively. (b) Illustration of the application of a spaced seed to match letters between a reference and a query sequence.

Supplementary Figure 2 Ratio of main memory accesses.

The ratio K/K’ as a function of the total length of the query sequences, for different seed lengths. The variables K and K’ represent the approximate number of main memory accesses required when using a single index or double index, respectively.

Supplementary Figure 3 PCoA analysis of 12 permafrost samples based on a subset of 6 million reads.

BLASTX results are shown on the left, (a) and (c). DIAMOND-fast results are shown on the right, (b) and (d). The upper two panels show the first and second principle coordinates, whereas the lower two panels show the first and third principle coordinates.

Source data

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Tables 1–3 (PDF 523 kb)

Supplementary Software

DIAMOND v0.4.7 source code (ZIP 2737 kb)

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Buchfink, B., Xie, C. & Huson, D. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015). https://doi.org/10.1038/nmeth.3176

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