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A multi-task convolutional deep neural network for variant calling in single molecule sequencing

Author

Listed:
  • Ruibang Luo

    (The University of Hong Kong
    Johns Hopkins University)

  • Fritz J. Sedlazeck

    (Baylor College of Medicine)

  • Tak-Wah Lam

    (The University of Hong Kong)

  • Michael C. Schatz

    (Johns Hopkins University)

Abstract

The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5–15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieves 99.67, 95.78, 90.53% F1-score on 1KP common variants, and 98.65, 92.57, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than 2 h on a standard server. Furthermore, we present 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source ( https://github.com/aquaskyline/Clairvoyante ), with modules to train, utilize and visualize the model.

Suggested Citation

  • Ruibang Luo & Fritz J. Sedlazeck & Tak-Wah Lam & Michael C. Schatz, 2019. "A multi-task convolutional deep neural network for variant calling in single molecule sequencing," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09025-z
    DOI: 10.1038/s41467-019-09025-z
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    Cited by:

    1. Fan Nie & Peng Ni & Neng Huang & Jun Zhang & Zhenyu Wang & Chuanle Xiao & Feng Luo & Jianxin Wang, 2024. "De novo diploid genome assembly using long noisy reads," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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