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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Nature Methods volume 14, pages 1072–1074 (2017)Cite this article

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Abstract

We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.

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Figure 1: Principle and property of DDF scoring algorithm in MECAT alignment.

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Sequence Read Archive

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Acknowledgements

We thank D.P. Wang for supplying the Chinese human data set. We thank the NCBI assembly group for the Han-1 Chinese annotation. This work was collectively supported by the National Natural Science Foundation of China (31471232, 31471789 and 31600667), the Fundamental Research Funds for the Central Universities (15ykjc23d), the Guangdong Natural Science Foundation (2015A030313127), the Joint Research Fund for the Overseas Natural Science of China (3030901001222), infrastructure support from Center for Precision Medicine (Sun Yat-sen University), China Postdoctoral Science Foundation (2017M612798), and the National Institute of Food and Agriculture (NIFA), USA (2017-70016-26051).

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Author notes

  1. Chuan-Le Xiao and Ying Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China

    Chuan-Le Xiao, Shang-Qian Xie, Kai-Ning Chen, Yan Wang, Yue Han & Zhi Xie

  2. School of Data and Computer Science, and Guangdong Provincial Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China

    Chuan-Le Xiao & Ying Chen

  3. Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Hunan, China

    Chuan-Le Xiao

  4. College of Plant Protection, Hunan Agricultural University, Changsha, China

    Chuan-Le Xiao

  5. Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China

    Shang-Qian Xie

  6. CookGene Bio-technology Co., Ltd., Guangzhou, China

    Yue Han

  7. School of Computing, Clemson University, Clemson, South Carolina, USA

    Feng Luo

Authors
  1. Chuan-Le Xiao
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  2. Ying Chen
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  3. Shang-Qian Xie
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  4. Kai-Ning Chen
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  5. Yan Wang
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  6. Yue Han
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  7. Feng Luo
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  8. Zhi Xie
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Contributions

C.-L.X. conceived and designed this project. Y.C. and C.-L.X. implemented the algorithms. S.-Q.X., C.L.-X., and Y.C. performed the test experiments. K.-N.C., Y.W., and Y.H. coordinated the data release and assisted with executing the pipeline. F.L. provided theoretical analysis of the algorithms. C.-L.X., F.L., Z.X., Y.C., and S.-Q.X. wrote the manuscript. All authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Chuan-Le Xiao, Feng Luo or Zhi Xie.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Notes 1–11 and Supplementary Tables 1, 2, 3, 5 and 6.

Life Sciences Reporting Summary

Supplementary Table 4

The read coverage of human reference genome alignment by BLASR and MECAT around regions with large structural variants

Supplementary Table 7

Comparison of Read Coverage of Reference Genome Alignment at Large Structural Variants

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Xiao, CL., Chen, Y., Xie, SQ. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat Methods 14, 1072–1074 (2017). https://doi.org/10.1038/nmeth.4432

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